From arokem at uw.edu  Thu Jul  1 13:08:04 2021
From: arokem at uw.edu (Ariel Rokem)
Date: Thu, 1 Jul 2021 10:08:04 -0700
Subject: [Neuroimaging] dipy has problem
In-Reply-To: <903b27f31057f05da43dd51a895e04cc@ut.ac.ir>
References: <903b27f31057f05da43dd51a895e04cc@ut.ac.ir>
Message-ID: <CA+X4w0w3GjU8R06NUTt6+hYEx=X8R7UxLZw3wzgt+ryzMY+tXQ@mail.gmail.com>

Hi Somaye,

Thanks for your email. First of all, you'd be better off directing future
questions about DIPY to this mailing list:
https://mail.python.org/mailman3/lists/dipy.python.org/.

Second, installation of DIPY includes the installation of some
Cython-compiled components (including recspeed, which you mentioned). If
it's possible, I would recommend initially installing with a
package manager, instead of directly from the source code. We support use
of `conda` as well as `pip`. See
https://dipy.org/documentation/1.4.1./installation/ for details.

Cheers,

Ariel

On Thu, Jul 1, 2021 at 10:03 AM sjabari <sjabari at ut.ac.ir> wrote:

> Dear,
>
> I installed Dipy(with the command: python setup.py install)  on windows
> 8.1 but I have error "ModuleNotFoundError: No module named
> 'dipy.reconst.recspeed' ".
>
> I saw the installation folder and found that "recspeed.py" file doesn't
> exist in reconst folder.
>
> What can I do?
>
> thanks,
>
> Somaye Jabari
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From matthew.brett at gmail.com  Tue Jul  6 06:06:19 2021
From: matthew.brett at gmail.com (Matthew Brett)
Date: Tue, 6 Jul 2021 11:06:19 +0100
Subject: [Neuroimaging] Nibabel CZI grant - starting work
Message-ID: <CAH6Pt5o1QzgHVTkmf61m-GQpjmjvOU2VwHSu7szmWobzMe8t9Q@mail.gmail.com>

Dear all,

You?ve already heard echoes about this on the list, but Nibabel now
has a Chan Zuckerberg Initiative grant from their Essential
Open-source Software for Science series.

All the details are here:

https://github.com/matthew-brett/czi-nibabel

We actually got the grant back in October last year, to start in
January, but I (Matthew) had some trouble negotiating time for the
work.  That is now resolved and we have the money ready to spend, and
the time to work on it.

We are planning to get going on the grant work starting this week
(starting 5 July).  You can see the general schedule in the work plan
in the Github repo above.  In particular, we will get going on the
planned milestones:

https://github.com/matthew-brett/czi-nibabel/blob/master/milestones.md

I will be starting work on the axis labelling / metadata API, and
better DICOM integration.  Chris will be ramping up work on the
surface API.  Oscar will be extending the surface transform work.

We?re emailing now to warn you that you will see more activity appear
quite quickly, and we would really appreciate help in reviewing. We
would love to hear from any of you who have particular interest in
these topics.

Cheers,

Matthew, Chris, Oscar

From satra at mit.edu  Tue Jul  6 06:57:21 2021
From: satra at mit.edu (Satrajit Ghosh)
Date: Tue, 6 Jul 2021 06:57:21 -0400
Subject: [Neuroimaging] Nibabel CZI grant - starting work
In-Reply-To: <CAH6Pt5o1QzgHVTkmf61m-GQpjmjvOU2VwHSu7szmWobzMe8t9Q@mail.gmail.com>
References: <CAH6Pt5o1QzgHVTkmf61m-GQpjmjvOU2VwHSu7szmWobzMe8t9Q@mail.gmail.com>
Message-ID: <CA+A4wOk+1yJRExXj_YpTOnkc-a1QNLo0R9muxRRXGcZJGaAK6g@mail.gmail.com>

congrats folks.

look forward to these new improvements in nibabel.

cheers,

satra

On Tue, Jul 6, 2021 at 6:07 AM Matthew Brett <matthew.brett at gmail.com>
wrote:

> Dear all,
>
> You?ve already heard echoes about this on the list, but Nibabel now
> has a Chan Zuckerberg Initiative grant from their Essential
> Open-source Software for Science series.
>
> All the details are here:
>
> https://github.com/matthew-brett/czi-nibabel
>
> We actually got the grant back in October last year, to start in
> January, but I (Matthew) had some trouble negotiating time for the
> work.  That is now resolved and we have the money ready to spend, and
> the time to work on it.
>
> We are planning to get going on the grant work starting this week
> (starting 5 July).  You can see the general schedule in the work plan
> in the Github repo above.  In particular, we will get going on the
> planned milestones:
>
> https://github.com/matthew-brett/czi-nibabel/blob/master/milestones.md
>
> I will be starting work on the axis labelling / metadata API, and
> better DICOM integration.  Chris will be ramping up work on the
> surface API.  Oscar will be extending the surface transform work.
>
> We?re emailing now to warn you that you will see more activity appear
> quite quickly, and we would really appreciate help in reviewing. We
> would love to hear from any of you who have particular interest in
> these topics.
>
> Cheers,
>
> Matthew, Chris, Oscar
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From demian.wassermann at inria.fr  Tue Jul  6 07:23:00 2021
From: demian.wassermann at inria.fr (Demian Wassermann)
Date: Tue, 6 Jul 2021 13:23:00 +0200
Subject: [Neuroimaging] Nibabel CZI grant - starting work
In-Reply-To: <CAH6Pt5o1QzgHVTkmf61m-GQpjmjvOU2VwHSu7szmWobzMe8t9Q@mail.gmail.com>
References: <CAH6Pt5o1QzgHVTkmf61m-GQpjmjvOU2VwHSu7szmWobzMe8t9Q@mail.gmail.com>
Message-ID: <5F0124C4-08FE-46D1-A9F5-FD26954E3AEB@inria.fr>

Sounds great!

Looking forward! And happy to help if needed. 

One thing that?s interesting is that, if I don?t remember it badly, MNIC format is actually a wrapper on HDF5

D
--
Demian Wassermann, PhD, HdR
demian.wassermann at inria.fr
Associate Research Professor (CRCN)
Parietal Team
INRIA Saclay Ile-de-France
1 Rue Honor? d'Estienne d'Orves, 91120 Palaiseau



> On 6 Jul 2021, at 12:06, Matthew Brett <matthew.brett at gmail.com> wrote:
> 
> Dear all,
> 
> You?ve already heard echoes about this on the list, but Nibabel now
> has a Chan Zuckerberg Initiative grant from their Essential
> Open-source Software for Science series.
> 
> All the details are here:
> 
> https://github.com/matthew-brett/czi-nibabel
> 
> We actually got the grant back in October last year, to start in
> January, but I (Matthew) had some trouble negotiating time for the
> work.  That is now resolved and we have the money ready to spend, and
> the time to work on it.
> 
> We are planning to get going on the grant work starting this week
> (starting 5 July).  You can see the general schedule in the work plan
> in the Github repo above.  In particular, we will get going on the
> planned milestones:
> 
> https://github.com/matthew-brett/czi-nibabel/blob/master/milestones.md
> 
> I will be starting work on the axis labelling / metadata API, and
> better DICOM integration.  Chris will be ramping up work on the
> surface API.  Oscar will be extending the surface transform work.
> 
> We?re emailing now to warn you that you will see more activity appear
> quite quickly, and we would really appreciate help in reviewing. We
> would love to hear from any of you who have particular interest in
> these topics.
> 
> Cheers,
> 
> Matthew, Chris, Oscar
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging

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From redhatw at gmail.com  Tue Jul  6 07:47:09 2021
From: redhatw at gmail.com (Ze Wang)
Date: Tue, 06 Jul 2021 11:47:09 +0000
Subject: [Neuroimaging] Nibabel CZI grant - starting work
In-Reply-To: <CAH6Pt5o1QzgHVTkmf61m-GQpjmjvOU2VwHSu7szmWobzMe8t9Q@mail.gmail.com>
References: <CAH6Pt5o1QzgHVTkmf61m-GQpjmjvOU2VwHSu7szmWobzMe8t9Q@mail.gmail.com>
Message-ID: <emd5253afa-55de-472a-86f2-2f849e8a21be@laptop-cm30trfu>

Excellent! Congratulations!

Ze

------ Original Message ------
From: "Matthew Brett" <matthew.brett at gmail.com>
To: "neuroimaging" <neuroimaging at python.org>
Sent: 7/6/2021 6:06:19 AM
Subject: [Neuroimaging] Nibabel CZI grant - starting work

>Dear all,
>
>You?ve already heard echoes about this on the list, but Nibabel now
>has a Chan Zuckerberg Initiative grant from their Essential
>Open-source Software for Science series.
>
>All the details are here:
>
>https://github.com/matthew-brett/czi-nibabel
>
>We actually got the grant back in October last year, to start in
>January, but I (Matthew) had some trouble negotiating time for the
>work.  That is now resolved and we have the money ready to spend, and
>the time to work on it.
>
>We are planning to get going on the grant work starting this week
>(starting 5 July).  You can see the general schedule in the work plan
>in the Github repo above.  In particular, we will get going on the
>planned milestones:
>
>https://github.com/matthew-brett/czi-nibabel/blob/master/milestones.md
>
>I will be starting work on the axis labelling / metadata API, and
>better DICOM integration.  Chris will be ramping up work on the
>surface API.  Oscar will be extending the surface transform work.
>
>We?re emailing now to warn you that you will see more activity appear
>quite quickly, and we would really appreciate help in reviewing. We
>would love to hear from any of you who have particular interest in
>these topics.
>
>Cheers,
>
>Matthew, Chris, Oscar
>_______________________________________________
>Neuroimaging mailing list
>Neuroimaging at python.org
>https://mail.python.org/mailman/listinfo/neuroimaging


From elef at indiana.edu  Tue Jul  6 09:26:44 2021
From: elef at indiana.edu (Eleftherios Garyfallidis)
Date: Tue, 6 Jul 2021 09:26:44 -0400
Subject: [Neuroimaging] Nibabel CZI grant - starting work
In-Reply-To: <emd5253afa-55de-472a-86f2-2f849e8a21be@laptop-cm30trfu>
References: <CAH6Pt5o1QzgHVTkmf61m-GQpjmjvOU2VwHSu7szmWobzMe8t9Q@mail.gmail.com>
 <emd5253afa-55de-472a-86f2-2f849e8a21be@laptop-cm30trfu>
Message-ID: <CAN6JmWNYA91RhZ8VamJS9DNK9wNt81tfJQzqQxpfeBTEYitMPg@mail.gmail.com>

Exciting. Will be happy to help review.

On Tue, Jul 6, 2021 at 7:47 AM Ze Wang <redhatw at gmail.com> wrote:

> Excellent! Congratulations!
>
> Ze
>
> ------ Original Message ------
> From: "Matthew Brett" <matthew.brett at gmail.com>
> To: "neuroimaging" <neuroimaging at python.org>
> Sent: 7/6/2021 6:06:19 AM
> Subject: [Neuroimaging] Nibabel CZI grant - starting work
>
> >Dear all,
> >
> >You?ve already heard echoes about this on the list, but Nibabel now
> >has a Chan Zuckerberg Initiative grant from their Essential
> >Open-source Software for Science series.
> >
> >All the details are here:
> >
> >https://github.com/matthew-brett/czi-nibabel
> >
> >We actually got the grant back in October last year, to start in
> >January, but I (Matthew) had some trouble negotiating time for the
> >work.  That is now resolved and we have the money ready to spend, and
> >the time to work on it.
> >
> >We are planning to get going on the grant work starting this week
> >(starting 5 July).  You can see the general schedule in the work plan
> >in the Github repo above.  In particular, we will get going on the
> >planned milestones:
> >
> >https://github.com/matthew-brett/czi-nibabel/blob/master/milestones.md
> >
> >I will be starting work on the axis labelling / metadata API, and
> >better DICOM integration.  Chris will be ramping up work on the
> >surface API.  Oscar will be extending the surface transform work.
> >
> >We?re emailing now to warn you that you will see more activity appear
> >quite quickly, and we would really appreciate help in reviewing. We
> >would love to hear from any of you who have particular interest in
> >these topics.
> >
> >Cheers,
> >
> >Matthew, Chris, Oscar
> >_______________________________________________
> >Neuroimaging mailing list
> >Neuroimaging at python.org
> >https://mail.python.org/mailman/listinfo/neuroimaging
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From jbpoline at gmail.com  Tue Jul  6 09:51:52 2021
From: jbpoline at gmail.com (JB Poline)
Date: Tue, 6 Jul 2021 09:51:52 -0400
Subject: [Neuroimaging] Nibabel CZI grant - starting work
In-Reply-To: <CAN6JmWNYA91RhZ8VamJS9DNK9wNt81tfJQzqQxpfeBTEYitMPg@mail.gmail.com>
References: <CAH6Pt5o1QzgHVTkmf61m-GQpjmjvOU2VwHSu7szmWobzMe8t9Q@mail.gmail.com>
 <emd5253afa-55de-472a-86f2-2f849e8a21be@laptop-cm30trfu>
 <CAN6JmWNYA91RhZ8VamJS9DNK9wNt81tfJQzqQxpfeBTEYitMPg@mail.gmail.com>
Message-ID: <CALMaa80r+pyRdBOWDV_4Puapu4E-F_2ov3-9UzEmcFTUpKcEuw@mail.gmail.com>

It's really good news !
JB


On Tue, Jul 6, 2021 at 9:27 AM Eleftherios Garyfallidis <elef at indiana.edu>
wrote:

> Exciting. Will be happy to help review.
>
> On Tue, Jul 6, 2021 at 7:47 AM Ze Wang <redhatw at gmail.com> wrote:
>
>> Excellent! Congratulations!
>>
>> Ze
>>
>> ------ Original Message ------
>> From: "Matthew Brett" <matthew.brett at gmail.com>
>> To: "neuroimaging" <neuroimaging at python.org>
>> Sent: 7/6/2021 6:06:19 AM
>> Subject: [Neuroimaging] Nibabel CZI grant - starting work
>>
>> >Dear all,
>> >
>> >You?ve already heard echoes about this on the list, but Nibabel now
>> >has a Chan Zuckerberg Initiative grant from their Essential
>> >Open-source Software for Science series.
>> >
>> >All the details are here:
>> >
>> >https://github.com/matthew-brett/czi-nibabel
>> >
>> >We actually got the grant back in October last year, to start in
>> >January, but I (Matthew) had some trouble negotiating time for the
>> >work.  That is now resolved and we have the money ready to spend, and
>> >the time to work on it.
>> >
>> >We are planning to get going on the grant work starting this week
>> >(starting 5 July).  You can see the general schedule in the work plan
>> >in the Github repo above.  In particular, we will get going on the
>> >planned milestones:
>> >
>> >https://github.com/matthew-brett/czi-nibabel/blob/master/milestones.md
>> >
>> >I will be starting work on the axis labelling / metadata API, and
>> >better DICOM integration.  Chris will be ramping up work on the
>> >surface API.  Oscar will be extending the surface transform work.
>> >
>> >We?re emailing now to warn you that you will see more activity appear
>> >quite quickly, and we would really appreciate help in reviewing. We
>> >would love to hear from any of you who have particular interest in
>> >these topics.
>> >
>> >Cheers,
>> >
>> >Matthew, Chris, Oscar
>> >_______________________________________________
>> >Neuroimaging mailing list
>> >Neuroimaging at python.org
>> >https://mail.python.org/mailman/listinfo/neuroimaging
>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From rimsham97 at gmail.com  Tue Jul  6 15:10:28 2021
From: rimsham97 at gmail.com (Rimsha Mahrukh)
Date: Wed, 7 Jul 2021 03:10:28 +0800
Subject: [Neuroimaging] code
Message-ID: <CAEzF3qtSfJh=L2+dg=mV9nqfMMDGn5O2ragQs6=RwGdezc1_Cg@mail.gmail.com>

Respected Sir/Madam,

I am sending you this mail because I needed some help with implementation.
I want to extract the first 30 mins from my FMRI bold run which is in 'nii'
format. As I apply the get_fdata() function on it I get a memory error. I
would be very thankful if you can guide me with this please.

Regards,
Rimsha
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From matthew.brett at gmail.com  Tue Jul  6 16:59:10 2021
From: matthew.brett at gmail.com (Matthew Brett)
Date: Tue, 6 Jul 2021 21:59:10 +0100
Subject: [Neuroimaging] code
In-Reply-To: <CAEzF3qtSfJh=L2+dg=mV9nqfMMDGn5O2ragQs6=RwGdezc1_Cg@mail.gmail.com>
References: <CAEzF3qtSfJh=L2+dg=mV9nqfMMDGn5O2ragQs6=RwGdezc1_Cg@mail.gmail.com>
Message-ID: <CAH6Pt5rhoGAjJ2GgA6wLiPo9+3Wdh6DxWJu9e34z+UJw=E957A@mail.gmail.com>

Hi,

On Tue, Jul 6, 2021 at 9:53 PM Rimsha Mahrukh <rimsham97 at gmail.com> wrote:
>
> Respected Sir/Madam,
>
> I am sending you this mail because I needed some help with implementation. I want to extract the first 30 mins from my FMRI bold run which is in 'nii' format. As I apply the get_fdata() function on it I get a memory error. I would be very thankful if you can guide me with this please.

Did you find:

https://nipy.org/nibabel/images_and_memory.html

?   Say your TR was 2 seconds, then the first 30 minutes are:

n_trs = int(30 * 60 / 2)

Then:

import nibabel as nib

# Does not load image into memory
img = nib.load('my_image.nii')

# Slice data object, still does not read into memory
data_30 = img.dataobj[..., :n_trs]

# Make a new image object
img_30 = nib.Nifti1Image(data_30, img.affine, img.header)

# Load these data
img_arr = img_30.get_fdata()

Does that work?

Cheers,

Matthew

From bertrand.thirion at inria.fr  Wed Jul  7 03:28:30 2021
From: bertrand.thirion at inria.fr (Bertrand Thirion)
Date: Wed, 7 Jul 2021 09:28:30 +0200 (CEST)
Subject: [Neuroimaging] Nibabel CZI grant - starting work
In-Reply-To: <CAH6Pt5o1QzgHVTkmf61m-GQpjmjvOU2VwHSu7szmWobzMe8t9Q@mail.gmail.com>
References: <CAH6Pt5o1QzgHVTkmf61m-GQpjmjvOU2VwHSu7szmWobzMe8t9Q@mail.gmail.com>
Message-ID: <450435271.488503.1625642910613.JavaMail.zimbra@inria.fr>

Congratulations ! 

Bertrand Thirion
Head of science (d?l?gu? scientifique) Inria Saclay-?le-de-France
Head of Parietal Team
Neurospin, CEA Saclay, 91191 Gif sur Yvette
+33 1 69 08 79 92
http://pages.saclay.inria.fr/bertrand.thirion

----- Mail original -----
> De: "matthew" <matthew.brett at gmail.com>
> ?: "Neuroimaging analysis in Python" <neuroimaging at python.org>
> Envoy?: Mardi 6 Juillet 2021 12:06:19
> Objet: [Neuroimaging] Nibabel CZI grant - starting work

> Dear all,
> 
> You?ve already heard echoes about this on the list, but Nibabel now
> has a Chan Zuckerberg Initiative grant from their Essential
> Open-source Software for Science series.
> 
> All the details are here:
> 
> https://github.com/matthew-brett/czi-nibabel
> 
> We actually got the grant back in October last year, to start in
> January, but I (Matthew) had some trouble negotiating time for the
> work.  That is now resolved and we have the money ready to spend, and
> the time to work on it.
> 
> We are planning to get going on the grant work starting this week
> (starting 5 July).  You can see the general schedule in the work plan
> in the Github repo above.  In particular, we will get going on the
> planned milestones:
> 
> https://github.com/matthew-brett/czi-nibabel/blob/master/milestones.md
> 
> I will be starting work on the axis labelling / metadata API, and
> better DICOM integration.  Chris will be ramping up work on the
> surface API.  Oscar will be extending the surface transform work.
> 
> We?re emailing now to warn you that you will see more activity appear
> quite quickly, and we would really appreciate help in reviewing. We
> would love to hear from any of you who have particular interest in
> these topics.
> 
> Cheers,
> 
> Matthew, Chris, Oscar
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging

From rolandomasisobando at gmail.com  Wed Jul  7 16:57:53 2021
From: rolandomasisobando at gmail.com (Rolando Masis-Obando)
Date: Wed, 7 Jul 2021 16:57:53 -0400
Subject: [Neuroimaging] pysurfer installation issue with python3 [Library
 not loaded: @rpath/libtbb.dylib]
Message-ID: <CAAG5-HpSQVOYV+ozd_SPdx+3_N28oT_cKjk31q+wTbrove5B8w@mail.gmail.com>

Hello,

I am unfortunately having trouble installing pysurfer on a mac Sierra
10.12.6

I've installed anaconda navigator to get all the dependencies working. I've
tried multiple different python versions and still no luck. To keep things
simple, I would like help with installing psyurfer on python 3.6. I used
these instructions
https://gist.github.com/danjgale/4f64ca81f5e91cc0669d0f744c7a9f82 to
install until I hit a roadblock.

This is the error I get:





































*>>> import vtkTraceback (most recent call last):  File
"/Users/amennen/anaconda3/envs/pysurfer/lib/python3.6/site-packages/vtkmodules/vtkCommonCore.py",
line 5, in <module>    from .vtkCommonCorePython import *ImportError:
dlopen(/Users/amennen/anaconda3/envs/pysurfer/lib/python3.6/site-packages/vtkmodules/vtkCommonCorePython.so,
2): Library not loaded: @rpath/libtbb.dylib  Referenced from:
/Users/amennen/anaconda3/envs/pysurfer/lib/libvtkCommonCorePython36D-8.2.1.dylib
Reason: image not foundDuring handling of the above exception, another
exception occurred:Traceback (most recent call last):  File "<stdin>", line
1, in <module>  File
"/Users/amennen/anaconda3/envs/pysurfer/lib/python3.6/site-packages/vtk.py",
line 32, in <module>    all_spec.loader.exec_module(all_m)  File
"/Users/amennen/anaconda3/envs/pysurfer/lib/python3.6/site-packages/vtkmodules/all.py",
line 7, in <module>    from .vtkCommonCore import *  File
"/Users/amennen/anaconda3/envs/pysurfer/lib/python3.6/site-packages/vtkmodules/vtkCommonCore.py",
line 9, in <module>    from vtkCommonCorePython import *ImportError:
dlopen(/Users/amennen/anaconda3/envs/pysurfer/lib/python3.6/site-packages/vtkmodules/vtkCommonCorePython.so,
2): Library not loaded: @rpath/libtbb.dylib  Referenced from:
/Users/amennen/anaconda3/envs/pysurfer/lib/libvtkCommonCorePython36D-8.2.1.dylib
Reason: image not found*

I've added the vtkmodules to the path:

>>> echo $PYTHONPATH

:/Users/amennen/anaconda3/envs/pysurfer/lib/python3.6/site-packages/vtkmodules


Does anyone have an easy way to install pysurfer? Unfortunately, I have not
had a lot of luck installing pysurfer on different computers, the issues
that come up are slightly different every time. Any help would be deeply
appreciated!

Thank you so much!

Best,
Rolando
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From z.baratz at gmail.com  Thu Jul  8 08:24:03 2021
From: z.baratz at gmail.com (Zvi Baratz)
Date: Thu, 8 Jul 2021 15:24:03 +0300
Subject: [Neuroimaging] Nibabel CZI grant - starting work
In-Reply-To: <CAH6Pt5o1QzgHVTkmf61m-GQpjmjvOU2VwHSu7szmWobzMe8t9Q@mail.gmail.com>
References: <CAH6Pt5o1QzgHVTkmf61m-GQpjmjvOU2VwHSu7szmWobzMe8t9Q@mail.gmail.com>
Message-ID: <CANJsFRZ2Vurz=4sfska6VOGprb+0JB3qZKYGe3ZMG+xfznmqXg@mail.gmail.com>

Hi all,

An open Zoom meeting on the topic of DICOM integration in NiBabel will be
held this coming Friday at 11:00 AM. Join us at this
<https://us02web.zoom.us/j/87473444050> address.

Best,
Zvi

On Tue, Jul 6, 2021, 13:07 Matthew Brett <matthew.brett at gmail.com> wrote:

> Dear all,
>
> You?ve already heard echoes about this on the list, but Nibabel now
> has a Chan Zuckerberg Initiative grant from their Essential
> Open-source Software for Science series.
>
> All the details are here:
>
> https://github.com/matthew-brett/czi-nibabel
>
> We actually got the grant back in October last year, to start in
> January, but I (Matthew) had some trouble negotiating time for the
> work.  That is now resolved and we have the money ready to spend, and
> the time to work on it.
>
> We are planning to get going on the grant work starting this week
> (starting 5 July).  You can see the general schedule in the work plan
> in the Github repo above.  In particular, we will get going on the
> planned milestones:
>
> https://github.com/matthew-brett/czi-nibabel/blob/master/milestones.md
>
> I will be starting work on the axis labelling / metadata API, and
> better DICOM integration.  Chris will be ramping up work on the
> surface API.  Oscar will be extending the surface transform work.
>
> We?re emailing now to warn you that you will see more activity appear
> quite quickly, and we would really appreciate help in reviewing. We
> would love to hear from any of you who have particular interest in
> these topics.
>
> Cheers,
>
> Matthew, Chris, Oscar
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From garyfallidis at gmail.com  Thu Jul  8 09:43:08 2021
From: garyfallidis at gmail.com (Eleftherios Garyfallidis)
Date: Thu, 8 Jul 2021 09:43:08 -0400
Subject: [Neuroimaging] Nibabel CZI grant - starting work
In-Reply-To: <CANJsFRZ2Vurz=4sfska6VOGprb+0JB3qZKYGe3ZMG+xfznmqXg@mail.gmail.com>
References: <CAH6Pt5o1QzgHVTkmf61m-GQpjmjvOU2VwHSu7szmWobzMe8t9Q@mail.gmail.com>
 <CANJsFRZ2Vurz=4sfska6VOGprb+0JB3qZKYGe3ZMG+xfznmqXg@mail.gmail.com>
Message-ID: <CAN6JmWOLjhz8u+xwB4bPkXvsTe4jBcizrN1Xnh-_F+EMhgnfkg@mail.gmail.com>

What is the timezone for the meeting?

On Thu, Jul 8, 2021 at 8:24 AM Zvi Baratz <z.baratz at gmail.com> wrote:

> Hi all,
>
> An open Zoom meeting on the topic of DICOM integration in NiBabel will be
> held this coming Friday at 11:00 AM. Join us at this
> <https://us02web.zoom.us/j/87473444050> address.
>
> Best,
> Zvi
>
> On Tue, Jul 6, 2021, 13:07 Matthew Brett <matthew.brett at gmail.com> wrote:
>
>> Dear all,
>>
>> You?ve already heard echoes about this on the list, but Nibabel now
>> has a Chan Zuckerberg Initiative grant from their Essential
>> Open-source Software for Science series.
>>
>> All the details are here:
>>
>> https://github.com/matthew-brett/czi-nibabel
>>
>> We actually got the grant back in October last year, to start in
>> January, but I (Matthew) had some trouble negotiating time for the
>> work.  That is now resolved and we have the money ready to spend, and
>> the time to work on it.
>>
>> We are planning to get going on the grant work starting this week
>> (starting 5 July).  You can see the general schedule in the work plan
>> in the Github repo above.  In particular, we will get going on the
>> planned milestones:
>>
>> https://github.com/matthew-brett/czi-nibabel/blob/master/milestones.md
>>
>> I will be starting work on the axis labelling / metadata API, and
>> better DICOM integration.  Chris will be ramping up work on the
>> surface API.  Oscar will be extending the surface transform work.
>>
>> We?re emailing now to warn you that you will see more activity appear
>> quite quickly, and we would really appreciate help in reviewing. We
>> would love to hear from any of you who have particular interest in
>> these topics.
>>
>> Cheers,
>>
>> Matthew, Chris, Oscar
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From z.baratz at gmail.com  Thu Jul  8 09:58:29 2021
From: z.baratz at gmail.com (Zvi Baratz)
Date: Thu, 8 Jul 2021 16:58:29 +0300
Subject: [Neuroimaging] Nibabel CZI grant - starting work
In-Reply-To: <CAN6JmWOLjhz8u+xwB4bPkXvsTe4jBcizrN1Xnh-_F+EMhgnfkg@mail.gmail.com>
References: <CAH6Pt5o1QzgHVTkmf61m-GQpjmjvOU2VwHSu7szmWobzMe8t9Q@mail.gmail.com>
 <CANJsFRZ2Vurz=4sfska6VOGprb+0JB3qZKYGe3ZMG+xfznmqXg@mail.gmail.com>
 <CAN6JmWOLjhz8u+xwB4bPkXvsTe4jBcizrN1Xnh-_F+EMhgnfkg@mail.gmail.com>
Message-ID: <CANJsFRaYVfthK0imzQqv9QOgmLTLaCzZNTS143XS-EbyGeV5Eg@mail.gmail.com>

So sorry - 11:00 AM Pacific time.

On Thu, Jul 8, 2021 at 4:43 PM Eleftherios Garyfallidis <
garyfallidis at gmail.com> wrote:

> What is the timezone for the meeting?
>
> On Thu, Jul 8, 2021 at 8:24 AM Zvi Baratz <z.baratz at gmail.com> wrote:
>
>> Hi all,
>>
>> An open Zoom meeting on the topic of DICOM integration in NiBabel will be
>> held this coming Friday at 11:00 AM. Join us at this
>> <https://us02web.zoom.us/j/87473444050> address.
>>
>> Best,
>> Zvi
>>
>> On Tue, Jul 6, 2021, 13:07 Matthew Brett <matthew.brett at gmail.com> wrote:
>>
>>> Dear all,
>>>
>>> You?ve already heard echoes about this on the list, but Nibabel now
>>> has a Chan Zuckerberg Initiative grant from their Essential
>>> Open-source Software for Science series.
>>>
>>> All the details are here:
>>>
>>> https://github.com/matthew-brett/czi-nibabel
>>>
>>> We actually got the grant back in October last year, to start in
>>> January, but I (Matthew) had some trouble negotiating time for the
>>> work.  That is now resolved and we have the money ready to spend, and
>>> the time to work on it.
>>>
>>> We are planning to get going on the grant work starting this week
>>> (starting 5 July).  You can see the general schedule in the work plan
>>> in the Github repo above.  In particular, we will get going on the
>>> planned milestones:
>>>
>>> https://github.com/matthew-brett/czi-nibabel/blob/master/milestones.md
>>>
>>> I will be starting work on the axis labelling / metadata API, and
>>> better DICOM integration.  Chris will be ramping up work on the
>>> surface API.  Oscar will be extending the surface transform work.
>>>
>>> We?re emailing now to warn you that you will see more activity appear
>>> quite quickly, and we would really appreciate help in reviewing. We
>>> would love to hear from any of you who have particular interest in
>>> these topics.
>>>
>>> Cheers,
>>>
>>> Matthew, Chris, Oscar
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From elef at indiana.edu  Thu Jul  8 11:59:26 2021
From: elef at indiana.edu (Eleftherios Garyfallidis)
Date: Thu, 8 Jul 2021 11:59:26 -0400
Subject: [Neuroimaging] Nibabel CZI grant - starting work
In-Reply-To: <34ec734aa3c046078ff1047cf7d96467@DM5PR08MB3595.namprd08.prod.outlook.com>
References: <CAH6Pt5o1QzgHVTkmf61m-GQpjmjvOU2VwHSu7szmWobzMe8t9Q@mail.gmail.com>
 <CANJsFRZ2Vurz=4sfska6VOGprb+0JB3qZKYGe3ZMG+xfznmqXg@mail.gmail.com>
 <CAN6JmWOLjhz8u+xwB4bPkXvsTe4jBcizrN1Xnh-_F+EMhgnfkg@mail.gmail.com>
 <34ec734aa3c046078ff1047cf7d96467@DM5PR08MB3595.namprd08.prod.outlook.com>
Message-ID: <CAN6JmWPw36EJ5TfBMdAew5i0-f_t=m_sbkbGhOuYpgBDB+Sxfg@mail.gmail.com>

Thank you Zvi. Time works for me.

On Thu, Jul 8, 2021 at 9:59 AM Zvi Baratz <z.baratz at gmail.com> wrote:

> So sorry - 11:00 AM Pacific time.
>
> On Thu, Jul 8, 2021 at 4:43 PM Eleftherios Garyfallidis <
> garyfallidis at gmail.com> wrote:
>
>> What is the timezone for the meeting?
>>
>> On Thu, Jul 8, 2021 at 8:24 AM Zvi Baratz <z.baratz at gmail.com> wrote:
>>
>>> Hi all,
>>>
>>> An open Zoom meeting on the topic of DICOM integration in NiBabel will
>>> be held this coming Friday at 11:00 AM. Join us at this
>>> <https://us02web.zoom.us/j/87473444050> address.
>>>
>>> Best,
>>> Zvi
>>>
>>> On Tue, Jul 6, 2021, 13:07 Matthew Brett <matthew.brett at gmail.com>
>>> wrote:
>>>
>>>> Dear all,
>>>>
>>>> You?ve already heard echoes about this on the list, but Nibabel now
>>>> has a Chan Zuckerberg Initiative grant from their Essential
>>>> Open-source Software for Science series.
>>>>
>>>> All the details are here:
>>>>
>>>> https://github.com/matthew-brett/czi-nibabel
>>>>
>>>> We actually got the grant back in October last year, to start in
>>>> January, but I (Matthew) had some trouble negotiating time for the
>>>> work.  That is now resolved and we have the money ready to spend, and
>>>> the time to work on it.
>>>>
>>>> We are planning to get going on the grant work starting this week
>>>> (starting 5 July).  You can see the general schedule in the work plan
>>>> in the Github repo above.  In particular, we will get going on the
>>>> planned milestones:
>>>>
>>>> https://github.com/matthew-brett/czi-nibabel/blob/master/milestones.md
>>>>
>>>> I will be starting work on the axis labelling / metadata API, and
>>>> better DICOM integration.  Chris will be ramping up work on the
>>>> surface API.  Oscar will be extending the surface transform work.
>>>>
>>>> We?re emailing now to warn you that you will see more activity appear
>>>> quite quickly, and we would really appreciate help in reviewing. We
>>>> would love to hear from any of you who have particular interest in
>>>> these topics.
>>>>
>>>> Cheers,
>>>>
>>>> Matthew, Chris, Oscar
>>>> _______________________________________________
>>>> Neuroimaging mailing list
>>>> Neuroimaging at python.org
>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
>
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From romain.valabregue at upmc.fr  Fri Jul  9 03:25:28 2021
From: romain.valabregue at upmc.fr (VRomain)
Date: Fri, 9 Jul 2021 09:25:28 +0200
Subject: [Neuroimaging] Nibabel CZI grant - starting work
In-Reply-To: <CAH6Pt5o1QzgHVTkmf61m-GQpjmjvOU2VwHSu7szmWobzMe8t9Q@mail.gmail.com>
References: <CAH6Pt5o1QzgHVTkmf61m-GQpjmjvOU2VwHSu7szmWobzMe8t9Q@mail.gmail.com>
Message-ID: <f7cd0e1c-0acd-a285-ddc4-79cdfa7eb2c7@upmc.fr>

Hi

great to see new effort on dicom parsing, (among other)


Sorry if this is a bit off topic, but seeing those new effort on nibabel 
(and the milestone on spatial transform), I wonder if you could help to 
solve the nifti ambiguity due to the 2 affine stored in the header

Personnaly, I still do not understand, why this choice has been made, 
and especially? why nobody agree on the interpretation (using multiple 
software, it is easy to get silent bug just because of different sform 
and qform ...

So not sure what the solution, if one get stick to the nifty and the 
possibility to store 2 affines, (I guess one will always get into 
trouble at some point. But may on could encourage an uniform 
interpretation among software ?

Cheers

Romain


Le 06/07/2021 ? 12:06, Matthew Brett a ?crit?:
> Dear all,
>
> You?ve already heard echoes about this on the list, but Nibabel now
> has a Chan Zuckerberg Initiative grant from their Essential
> Open-source Software for Science series.
>
> All the details are here:
>
> https://github.com/matthew-brett/czi-nibabel
>
> We actually got the grant back in October last year, to start in
> January, but I (Matthew) had some trouble negotiating time for the
> work.  That is now resolved and we have the money ready to spend, and
> the time to work on it.
>
> We are planning to get going on the grant work starting this week
> (starting 5 July).  You can see the general schedule in the work plan
> in the Github repo above.  In particular, we will get going on the
> planned milestones:
>
> https://github.com/matthew-brett/czi-nibabel/blob/master/milestones.md
>
> I will be starting work on the axis labelling / metadata API, and
> better DICOM integration.  Chris will be ramping up work on the
> surface API.  Oscar will be extending the surface transform work.
>
> We?re emailing now to warn you that you will see more activity appear
> quite quickly, and we would really appreciate help in reviewing. We
> would love to hear from any of you who have particular interest in
> these topics.
>
> Cheers,
>
> Matthew, Chris, Oscar
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging

From code at oscaresteban.es  Fri Jul  9 03:55:26 2021
From: code at oscaresteban.es (Oscar Esteban)
Date: Fri, 9 Jul 2021 09:55:26 +0200
Subject: [Neuroimaging] Nibabel CZI grant - starting work
In-Reply-To: <f7cd0e1c-0acd-a285-ddc4-79cdfa7eb2c7@upmc.fr>
References: <CAH6Pt5o1QzgHVTkmf61m-GQpjmjvOU2VwHSu7szmWobzMe8t9Q@mail.gmail.com>
 <f7cd0e1c-0acd-a285-ddc4-79cdfa7eb2c7@upmc.fr>
Message-ID: <CAAsFcgx3Tr4h-gTiQKpDG7nPtjWPd7mc4Z3JaRVstO21JWPcfQ@mail.gmail.com>

Hi Romain,

I definitely recommend you send a fresh email to the list with your
question.

Long story short, having the possibility to store two affines in the NIfTI
header is actually a very clever idea. But, as often happens, if you then
don't fully implement that idea the result is confusing and even dangerous.

Happy to follow up in some other thread (or in the nitransforms repo -
https://github.com/poldracklab/nitransforms)

Cheer,
Oscar


On Fri, Jul 9, 2021 at 9:32 AM VRomain <romain.valabregue at upmc.fr> wrote:

> Hi
>
> great to see new effort on dicom parsing, (among other)
>
>
> Sorry if this is a bit off topic, but seeing those new effort on nibabel
> (and the milestone on spatial transform), I wonder if you could help to
> solve the nifti ambiguity due to the 2 affine stored in the header
>
> Personnaly, I still do not understand, why this choice has been made,
> and especially  why nobody agree on the interpretation (using multiple
> software, it is easy to get silent bug just because of different sform
> and qform ...
>
> So not sure what the solution, if one get stick to the nifty and the
> possibility to store 2 affines, (I guess one will always get into
> trouble at some point. But may on could encourage an uniform
> interpretation among software ?
>
> Cheers
>
> Romain
>
>
> Le 06/07/2021 ? 12:06, Matthew Brett a ?crit :
> > Dear all,
> >
> > You?ve already heard echoes about this on the list, but Nibabel now
> > has a Chan Zuckerberg Initiative grant from their Essential
> > Open-source Software for Science series.
> >
> > All the details are here:
> >
> > https://github.com/matthew-brett/czi-nibabel
> >
> > We actually got the grant back in October last year, to start in
> > January, but I (Matthew) had some trouble negotiating time for the
> > work.  That is now resolved and we have the money ready to spend, and
> > the time to work on it.
> >
> > We are planning to get going on the grant work starting this week
> > (starting 5 July).  You can see the general schedule in the work plan
> > in the Github repo above.  In particular, we will get going on the
> > planned milestones:
> >
> > https://github.com/matthew-brett/czi-nibabel/blob/master/milestones.md
> >
> > I will be starting work on the axis labelling / metadata API, and
> > better DICOM integration.  Chris will be ramping up work on the
> > surface API.  Oscar will be extending the surface transform work.
> >
> > We?re emailing now to warn you that you will see more activity appear
> > quite quickly, and we would really appreciate help in reviewing. We
> > would love to hear from any of you who have particular interest in
> > these topics.
> >
> > Cheers,
> >
> > Matthew, Chris, Oscar
> > _______________________________________________
> > Neuroimaging mailing list
> > Neuroimaging at python.org
> > https://mail.python.org/mailman/listinfo/neuroimaging
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From romain.valabregue at upmc.fr  Fri Jul  9 04:51:01 2021
From: romain.valabregue at upmc.fr (VRomain)
Date: Fri, 9 Jul 2021 10:51:01 +0200
Subject: [Neuroimaging] why 2 affine transforms in the nifti
Message-ID: <f54c4737-fc1e-f489-2056-300c9a1b86d5@upmc.fr>

Hello


As suggest by oscar I open a new thread, since there may be nothing to 
do with Nibabel CZI grant


So to resume, I sometimes get? troubles when playing with different 
software, because of the 2 affines stored in the nifti file.

(some software thing one should only read / write the sform, other the 
qform, so it is easy to get to inconsistency, that will just scratch 
your results)

Thanks @ oscar to point out the nitransforms repo - 
https://github.com/poldracklab/nitransforms 
<https://github.com/poldracklab/nitransforms>)

I'll have a closer look, this is indeed an important objectiv


I am curious, to know why it was a clever idea to store 2 affine ? ( I 
probably miss the point ... )

 From what I understand, it was meant to get an history of the 
registration made on the data. The only software I know that use it, is 
spm coregister function. they update the sform and keep the qform. Ok we 
can come back, but if for any reason one have to coregister a second 
time, then the information is lost (because they chose to update the 
sform, and the qform take the old sform value ...)


From demian.wassermann at inria.fr  Fri Jul  9 05:13:31 2021
From: demian.wassermann at inria.fr (Demian Wassermann)
Date: Fri, 9 Jul 2021 11:13:31 +0200
Subject: [Neuroimaging] why 2 affine transforms in the nifti
In-Reply-To: <f54c4737-fc1e-f489-2056-300c9a1b86d5@upmc.fr>
References: <f54c4737-fc1e-f489-2056-300c9a1b86d5@upmc.fr>
Message-ID: <2DE747CA-C241-46BA-BCD2-5D7BE11B3ABB@inria.fr>

Dear Romain,

I think that you refer to the qform and sform transforms. If I?m not wrong the main idea of storing these two transforms is that qform transforms between voxel space and subject space in mm, and that sform transforms between voxel space and a ?standard space? such as ACPC, or talairach (see https://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html ) so you?d encode the output of a linear registration towards such standard space. Then there is of course the issue of poor documentation and then the way the data is used despite the standard?s intent

Best
Demian
--
Demian Wassermann, PhD, HdR
demian.wassermann at inria.fr
Associate Research Professor (CRCN)
Parietal Team
INRIA Saclay Ile-de-France
1 Rue Honor? d'Estienne d'Orves, 91120 Palaiseau



> On 9 Jul 2021, at 10:51, VRomain <romain.valabregue at upmc.fr> wrote:
> 
> Hello
> 
> 
> As suggest by oscar I open a new thread, since there may be nothing to do with Nibabel CZI grant
> 
> 
> So to resume, I sometimes get  troubles when playing with different software, because of the 2 affines stored in the nifti file.
> 
> (some software thing one should only read / write the sform, other the qform, so it is easy to get to inconsistency, that will just scratch your results)
> 
> Thanks @ oscar to point out the nitransforms repo - https://github.com/poldracklab/nitransforms <https://github.com/poldracklab/nitransforms>)
> 
> I'll have a closer look, this is indeed an important objectiv
> 
> 
> I am curious, to know why it was a clever idea to store 2 affine ? ( I probably miss the point ... )
> 
> From what I understand, it was meant to get an history of the registration made on the data. The only software I know that use it, is spm coregister function. they update the sform and keep the qform. Ok we can come back, but if for any reason one have to coregister a second time, then the information is lost (because they chose to update the sform, and the qform take the old sform value ...)
> 
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging

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From romain.valabregue at upmc.fr  Fri Jul  9 07:06:58 2021
From: romain.valabregue at upmc.fr (VRomain)
Date: Fri, 9 Jul 2021 13:06:58 +0200
Subject: [Neuroimaging] why 2 affine transforms in the nifti
In-Reply-To: <2DE747CA-C241-46BA-BCD2-5D7BE11B3ABB@inria.fr>
References: <f54c4737-fc1e-f489-2056-300c9a1b86d5@upmc.fr>
 <2DE747CA-C241-46BA-BCD2-5D7BE11B3ABB@inria.fr>
Message-ID: <8a130e8d-aae6-6d05-734f-88f7b9901e34@upmc.fr>

Yes thanks for the reference, that is indeed the right place to start,

so ok it is recommended to use qform for the "subject space", and the 
sform for "standard space" but note that this is set by the 
[sq]form_code? and nothing prevent you to do the opposite of the 
recommendation with sform_code=1 and qform_code=2 for instance.

the doc, say you may need the both depending on the use case, but no way 
to know which one to use if both [sq]form_code are >0 (ok it is 
depending on the use case ...)


Just as an example of inconsistency, when you convert from dicom to 
nifti, you usually get both sform and qform set, with [sq]form_code to 
1. but if you write an image with sitk, only the qform is set.


Many coregistration tools (fsl, freesurfer, ants, niftireg) make the 
choice to do not change the nifti header and to write the coregistration 
affine in a separate file, so for them, I do not see a need of 2 affines 
... (this is the best choice to avoid any confusion, and then you can 
have as many registration to as many template you wish !)


Only spm (as far as I know), decide to change the nifti header after a 
coregistration. It has the advantage, that they then do not need to 
compose affine and non-linear registration (you can directly apply the 
non-linear field, because thanks to the header change, the affine 
registration is already applied) ... but even for that there is no need 
of 2 transform: (they could also change the affine, if there was only 
one in the header !)

is there any tools or use case, that need this 2 transforms ?


May be I am concern because I made the wrong choice to use spm 
coregister at the first place (old habit take time to change ...). When 
I mixt with other tools for other task, I may end up having problems ...

if you stay with other coregistration tool, you just do not care and 
stay with 2 identical affine stored in the header ...




Le 09/07/2021 ? 11:13, Demian Wassermann a ?crit?:
> Dear Romain,
>
> I think that you refer to the qform and sform transforms. If I?m not wrong the main idea of storing these two transforms is that qform transforms between voxel space and subject space in mm, and that sform transforms between voxel space and a ?standard space? such as ACPC, or talairach (see https://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html ) so you?d encode the output of a linear registration towards such standard space. Then there is of course the issue of poor documentation and then the way the data is used despite the standard?s intent
>
> Best
> Demian
> --
> Demian Wassermann, PhD, HdR
> demian.wassermann at inria.fr
> Associate Research Professor (CRCN)
> Parietal Team
> INRIA Saclay Ile-de-France
> 1 Rue Honor? d'Estienne d'Orves, 91120 Palaiseau
>
>
>
>> On 9 Jul 2021, at 10:51, VRomain <romain.valabregue at upmc.fr> wrote:
>>
>> Hello
>>
>>
>> As suggest by oscar I open a new thread, since there may be nothing to do with Nibabel CZI grant
>>
>>
>> So to resume, I sometimes get  troubles when playing with different software, because of the 2 affines stored in the nifti file.
>>
>> (some software thing one should only read / write the sform, other the qform, so it is easy to get to inconsistency, that will just scratch your results)
>>
>> Thanks @ oscar to point out the nitransforms repo - https://github.com/poldracklab/nitransforms <https://github.com/poldracklab/nitransforms>)
>>
>> I'll have a closer look, this is indeed an important objectiv
>>
>>
>> I am curious, to know why it was a clever idea to store 2 affine ? ( I probably miss the point ... )
>>
>>  From what I understand, it was meant to get an history of the registration made on the data. The only software I know that use it, is spm coregister function. they update the sform and keep the qform. Ok we can come back, but if for any reason one have to coregister a second time, then the information is lost (because they chose to update the sform, and the qform take the old sform value ...)
>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
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From matthew.brett at gmail.com  Sat Jul 10 10:42:53 2021
From: matthew.brett at gmail.com (Matthew Brett)
Date: Sat, 10 Jul 2021 15:42:53 +0100
Subject: [Neuroimaging] Discourse category for DICOM discussions
Message-ID: <CAH6Pt5om9-z_0ifofP=Gyfdkx+yrDirS9ysNUMxSk164sTsoaQ@mail.gmail.com>

Hi,

We had a good discussion yesterday about what to do next with Python and DICOM.

To keep the discussion going, while not overloading your inboxes, I've
asked Discourse for a Nipy Discourse instance, and I've made a
category for the DICOM discussions, here:

https://nipy.discourse.group/c/python-dicom

Can I suggest that we move the DICOM discussions to that category?
Then we can feed back here, from time to time.

The Discourse category is all public, so you can always go and see
what we are up to by following the link.  For those new to Discourse,
it's a rather nice Forum-like system that has good email integration,
and Markdown editing, so it's a nice way of making well-formed,
publicly searchable messages and discussions, that you can use via
email if you want.

If anyone wants new categories or admin permissions on the Discourse
instance, just let me know.

Cheers,

Matthew

From satra at mit.edu  Sat Jul 10 11:14:50 2021
From: satra at mit.edu (Satrajit Ghosh)
Date: Sat, 10 Jul 2021 11:14:50 -0400
Subject: [Neuroimaging] Discourse category for DICOM discussions
In-Reply-To: <CAH6Pt5om9-z_0ifofP=Gyfdkx+yrDirS9ysNUMxSk164sTsoaQ@mail.gmail.com>
References: <CAH6Pt5om9-z_0ifofP=Gyfdkx+yrDirS9ysNUMxSk164sTsoaQ@mail.gmail.com>
Message-ID: <CA+A4wOmOKPeA4vNLb-R-oG0MES=uCMM=Er72gPiUYB-P+Zm7nw@mail.gmail.com>

hi matthew,

any reason not to use neurostars for this (which is a discourse platform)?
a number of neuroimaging software discussions are already happening there,
including questions about nibabel and dicom conversion tools.

cheers,

satra

On Sat, Jul 10, 2021 at 10:43 AM Matthew Brett <matthew.brett at gmail.com>
wrote:

> Hi,
>
> We had a good discussion yesterday about what to do next with Python and
> DICOM.
>
> To keep the discussion going, while not overloading your inboxes, I've
> asked Discourse for a Nipy Discourse instance, and I've made a
> category for the DICOM discussions, here:
>
> https://nipy.discourse.group/c/python-dicom
>
> Can I suggest that we move the DICOM discussions to that category?
> Then we can feed back here, from time to time.
>
> The Discourse category is all public, so you can always go and see
> what we are up to by following the link.  For those new to Discourse,
> it's a rather nice Forum-like system that has good email integration,
> and Markdown editing, so it's a nice way of making well-formed,
> publicly searchable messages and discussions, that you can use via
> email if you want.
>
> If anyone wants new categories or admin permissions on the Discourse
> instance, just let me know.
>
> Cheers,
>
> Matthew
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From matthew.brett at gmail.com  Sat Jul 10 11:53:41 2021
From: matthew.brett at gmail.com (Matthew Brett)
Date: Sat, 10 Jul 2021 16:53:41 +0100
Subject: [Neuroimaging] Discourse category for DICOM discussions
In-Reply-To: <CA+A4wOmOKPeA4vNLb-R-oG0MES=uCMM=Er72gPiUYB-P+Zm7nw@mail.gmail.com>
References: <CAH6Pt5om9-z_0ifofP=Gyfdkx+yrDirS9ysNUMxSk164sTsoaQ@mail.gmail.com>
 <CA+A4wOmOKPeA4vNLb-R-oG0MES=uCMM=Er72gPiUYB-P+Zm7nw@mail.gmail.com>
Message-ID: <CAH6Pt5qVscEdWM=e7L55sr37jj10bY_NFPAAUav0nyHTb=rb=Q@mail.gmail.com>

Hi,

Ah - sorry - I didn't realize Neurostars was a Discourse instance - I
hadn't looked for ages.  No, no reason, let's move there.  How do I
create a new category?  Is there a system for collecting / archiving
the post data so that we can replicate it if there's a problem?

Cheers,

Matthew



On Sat, Jul 10, 2021 at 4:15 PM Satrajit Ghosh <satra at mit.edu> wrote:
>
> hi matthew,
>
> any reason not to use neurostars for this (which is a discourse platform)? a number of neuroimaging software discussions are already happening there, including questions about nibabel and dicom conversion tools.
>
> cheers,
>
> satra
>
> On Sat, Jul 10, 2021 at 10:43 AM Matthew Brett <matthew.brett at gmail.com> wrote:
>>
>> Hi,
>>
>> We had a good discussion yesterday about what to do next with Python and DICOM.
>>
>> To keep the discussion going, while not overloading your inboxes, I've
>> asked Discourse for a Nipy Discourse instance, and I've made a
>> category for the DICOM discussions, here:
>>
>> https://nipy.discourse.group/c/python-dicom
>>
>> Can I suggest that we move the DICOM discussions to that category?
>> Then we can feed back here, from time to time.
>>
>> The Discourse category is all public, so you can always go and see
>> what we are up to by following the link.  For those new to Discourse,
>> it's a rather nice Forum-like system that has good email integration,
>> and Markdown editing, so it's a nice way of making well-formed,
>> publicly searchable messages and discussions, that you can use via
>> email if you want.
>>
>> If anyone wants new categories or admin permissions on the Discourse
>> instance, just let me know.
>>
>> Cheers,
>>
>> Matthew
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging

From pieper at isomics.com  Sat Jul 10 12:05:20 2021
From: pieper at isomics.com (Steve Pieper)
Date: Sat, 10 Jul 2021 12:05:20 -0400
Subject: [Neuroimaging] Discourse category for DICOM discussions
In-Reply-To: <CAH6Pt5qVscEdWM=e7L55sr37jj10bY_NFPAAUav0nyHTb=rb=Q@mail.gmail.com>
References: <CAH6Pt5om9-z_0ifofP=Gyfdkx+yrDirS9ysNUMxSk164sTsoaQ@mail.gmail.com>
 <CA+A4wOmOKPeA4vNLb-R-oG0MES=uCMM=Er72gPiUYB-P+Zm7nw@mail.gmail.com>
 <CAH6Pt5qVscEdWM=e7L55sr37jj10bY_NFPAAUav0nyHTb=rb=Q@mail.gmail.com>
Message-ID: <CADkb7uPRmO-ACh0OAkNnfjuq0sABJnw7xg8goynFWVwgK-67Ng@mail.gmail.com>

Hi Mathew and Satra -

I'm sorry I couldn't attend the meeting yesterday, but I look forward to
this further discussion.  Are there any notes from the meeting?

Best,
Steve

On Sat, Jul 10, 2021 at 11:54 AM Matthew Brett <matthew.brett at gmail.com>
wrote:

> Hi,
>
> Ah - sorry - I didn't realize Neurostars was a Discourse instance - I
> hadn't looked for ages.  No, no reason, let's move there.  How do I
> create a new category?  Is there a system for collecting / archiving
> the post data so that we can replicate it if there's a problem?
>
> Cheers,
>
> Matthew
>
>
>
> On Sat, Jul 10, 2021 at 4:15 PM Satrajit Ghosh <satra at mit.edu> wrote:
> >
> > hi matthew,
> >
> > any reason not to use neurostars for this (which is a discourse
> platform)? a number of neuroimaging software discussions are already
> happening there, including questions about nibabel and dicom conversion
> tools.
> >
> > cheers,
> >
> > satra
> >
> > On Sat, Jul 10, 2021 at 10:43 AM Matthew Brett <matthew.brett at gmail.com>
> wrote:
> >>
> >> Hi,
> >>
> >> We had a good discussion yesterday about what to do next with Python
> and DICOM.
> >>
> >> To keep the discussion going, while not overloading your inboxes, I've
> >> asked Discourse for a Nipy Discourse instance, and I've made a
> >> category for the DICOM discussions, here:
> >>
> >> https://nipy.discourse.group/c/python-dicom
> >>
> >> Can I suggest that we move the DICOM discussions to that category?
> >> Then we can feed back here, from time to time.
> >>
> >> The Discourse category is all public, so you can always go and see
> >> what we are up to by following the link.  For those new to Discourse,
> >> it's a rather nice Forum-like system that has good email integration,
> >> and Markdown editing, so it's a nice way of making well-formed,
> >> publicly searchable messages and discussions, that you can use via
> >> email if you want.
> >>
> >> If anyone wants new categories or admin permissions on the Discourse
> >> instance, just let me know.
> >>
> >> Cheers,
> >>
> >> Matthew
> >> _______________________________________________
> >> Neuroimaging mailing list
> >> Neuroimaging at python.org
> >> https://mail.python.org/mailman/listinfo/neuroimaging
> >
> > _______________________________________________
> > Neuroimaging mailing list
> > Neuroimaging at python.org
> > https://mail.python.org/mailman/listinfo/neuroimaging
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From satra at mit.edu  Sat Jul 10 12:08:24 2021
From: satra at mit.edu (Satrajit Ghosh)
Date: Sat, 10 Jul 2021 12:08:24 -0400
Subject: [Neuroimaging] Discourse category for DICOM discussions
In-Reply-To: <CAH6Pt5qVscEdWM=e7L55sr37jj10bY_NFPAAUav0nyHTb=rb=Q@mail.gmail.com>
References: <CAH6Pt5om9-z_0ifofP=Gyfdkx+yrDirS9ysNUMxSk164sTsoaQ@mail.gmail.com>
 <CA+A4wOmOKPeA4vNLb-R-oG0MES=uCMM=Er72gPiUYB-P+Zm7nw@mail.gmail.com>
 <CAH6Pt5qVscEdWM=e7L55sr37jj10bY_NFPAAUav0nyHTb=rb=Q@mail.gmail.com>
Message-ID: <CA+A4wOnTkUeQsvo_KcOHgEA103PCokLK9VdzqJ=AwaVG6zw=jA@mail.gmail.com>

hi mathew,

categories are created by incf admins. in the past users were encouraged to
tags and post everything under neuroquestions, as we did not want to blow
up categories and everything could be searched through tags. for example:

https://neurostars.org/tag/nibabel

and here is an example of multi tag search.

https://neurostars.org/search?q=tag%3Acifti%20tag%3Anibabel

regarding back up, again we can ask this as a meta-question.

cheers,

satra

On Sat, Jul 10, 2021 at 11:54 AM Matthew Brett <matthew.brett at gmail.com>
wrote:

> Hi,
>
> Ah - sorry - I didn't realize Neurostars was a Discourse instance - I
> hadn't looked for ages.  No, no reason, let's move there.  How do I
> create a new category?  Is there a system for collecting / archiving
> the post data so that we can replicate it if there's a problem?
>
> Cheers,
>
> Matthew
>
>
>
> On Sat, Jul 10, 2021 at 4:15 PM Satrajit Ghosh <satra at mit.edu> wrote:
> >
> > hi matthew,
> >
> > any reason not to use neurostars for this (which is a discourse
> platform)? a number of neuroimaging software discussions are already
> happening there, including questions about nibabel and dicom conversion
> tools.
> >
> > cheers,
> >
> > satra
> >
> > On Sat, Jul 10, 2021 at 10:43 AM Matthew Brett <matthew.brett at gmail.com>
> wrote:
> >>
> >> Hi,
> >>
> >> We had a good discussion yesterday about what to do next with Python
> and DICOM.
> >>
> >> To keep the discussion going, while not overloading your inboxes, I've
> >> asked Discourse for a Nipy Discourse instance, and I've made a
> >> category for the DICOM discussions, here:
> >>
> >> https://nipy.discourse.group/c/python-dicom
> >>
> >> Can I suggest that we move the DICOM discussions to that category?
> >> Then we can feed back here, from time to time.
> >>
> >> The Discourse category is all public, so you can always go and see
> >> what we are up to by following the link.  For those new to Discourse,
> >> it's a rather nice Forum-like system that has good email integration,
> >> and Markdown editing, so it's a nice way of making well-formed,
> >> publicly searchable messages and discussions, that you can use via
> >> email if you want.
> >>
> >> If anyone wants new categories or admin permissions on the Discourse
> >> instance, just let me know.
> >>
> >> Cheers,
> >>
> >> Matthew
> >> _______________________________________________
> >> Neuroimaging mailing list
> >> Neuroimaging at python.org
> >> https://mail.python.org/mailman/listinfo/neuroimaging
> >
> > _______________________________________________
> > Neuroimaging mailing list
> > Neuroimaging at python.org
> > https://mail.python.org/mailman/listinfo/neuroimaging
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From matthew.brett at gmail.com  Sat Jul 10 12:09:20 2021
From: matthew.brett at gmail.com (Matthew Brett)
Date: Sat, 10 Jul 2021 17:09:20 +0100
Subject: [Neuroimaging] Discourse category for DICOM discussions
In-Reply-To: <CADkb7uPRmO-ACh0OAkNnfjuq0sABJnw7xg8goynFWVwgK-67Ng@mail.gmail.com>
References: <CAH6Pt5om9-z_0ifofP=Gyfdkx+yrDirS9ysNUMxSk164sTsoaQ@mail.gmail.com>
 <CA+A4wOmOKPeA4vNLb-R-oG0MES=uCMM=Er72gPiUYB-P+Zm7nw@mail.gmail.com>
 <CAH6Pt5qVscEdWM=e7L55sr37jj10bY_NFPAAUav0nyHTb=rb=Q@mail.gmail.com>
 <CADkb7uPRmO-ACh0OAkNnfjuq0sABJnw7xg8goynFWVwgK-67Ng@mail.gmail.com>
Message-ID: <CAH6Pt5q+u0u2NdxbXAgxswaJ4pcBQ_GLCDLN=nCbO61hx8jqVw@mail.gmail.com>

Hi Steve,

Some sparse notes here:

https://docs.google.com/document/d/1Ca999GAx1qfCT0Hw5JRlJSEJeVTRDYaIg1h1LWbgYoo/edit?usp=sharing

The next plan was to have a show-and-tell session where we go over the
main parts of the various Python libraries covering DICOM in
neuroimaging, which we so far have as:

dicom_parser
dcmstack
Nibabel/nicom

All welcome, as usual; any other suggestions welcome.  We haven't got
a time yet - I think Zvi had kindly agreed to poll and set that up
next week.

Cheers,

Matthew

On Sat, Jul 10, 2021 at 5:06 PM Steve Pieper <pieper at isomics.com> wrote:
>
> Hi Mathew and Satra -
>
> I'm sorry I couldn't attend the meeting yesterday, but I look forward to this further discussion.  Are there any notes from the meeting?
>
> Best,
> Steve
>
> On Sat, Jul 10, 2021 at 11:54 AM Matthew Brett <matthew.brett at gmail.com> wrote:
>>
>> Hi,
>>
>> Ah - sorry - I didn't realize Neurostars was a Discourse instance - I
>> hadn't looked for ages.  No, no reason, let's move there.  How do I
>> create a new category?  Is there a system for collecting / archiving
>> the post data so that we can replicate it if there's a problem?
>>
>> Cheers,
>>
>> Matthew
>>
>>
>>
>> On Sat, Jul 10, 2021 at 4:15 PM Satrajit Ghosh <satra at mit.edu> wrote:
>> >
>> > hi matthew,
>> >
>> > any reason not to use neurostars for this (which is a discourse platform)? a number of neuroimaging software discussions are already happening there, including questions about nibabel and dicom conversion tools.
>> >
>> > cheers,
>> >
>> > satra
>> >
>> > On Sat, Jul 10, 2021 at 10:43 AM Matthew Brett <matthew.brett at gmail.com> wrote:
>> >>
>> >> Hi,
>> >>
>> >> We had a good discussion yesterday about what to do next with Python and DICOM.
>> >>
>> >> To keep the discussion going, while not overloading your inboxes, I've
>> >> asked Discourse for a Nipy Discourse instance, and I've made a
>> >> category for the DICOM discussions, here:
>> >>
>> >> https://nipy.discourse.group/c/python-dicom
>> >>
>> >> Can I suggest that we move the DICOM discussions to that category?
>> >> Then we can feed back here, from time to time.
>> >>
>> >> The Discourse category is all public, so you can always go and see
>> >> what we are up to by following the link.  For those new to Discourse,
>> >> it's a rather nice Forum-like system that has good email integration,
>> >> and Markdown editing, so it's a nice way of making well-formed,
>> >> publicly searchable messages and discussions, that you can use via
>> >> email if you want.
>> >>
>> >> If anyone wants new categories or admin permissions on the Discourse
>> >> instance, just let me know.
>> >>
>> >> Cheers,
>> >>
>> >> Matthew
>> >> _______________________________________________
>> >> Neuroimaging mailing list
>> >> Neuroimaging at python.org
>> >> https://mail.python.org/mailman/listinfo/neuroimaging
>> >
>> > _______________________________________________
>> > Neuroimaging mailing list
>> > Neuroimaging at python.org
>> > https://mail.python.org/mailman/listinfo/neuroimaging
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging

From matthew.brett at gmail.com  Sat Jul 10 12:29:20 2021
From: matthew.brett at gmail.com (Matthew Brett)
Date: Sat, 10 Jul 2021 17:29:20 +0100
Subject: [Neuroimaging] Discourse category for DICOM discussions
In-Reply-To: <CA+A4wOnTkUeQsvo_KcOHgEA103PCokLK9VdzqJ=AwaVG6zw=jA@mail.gmail.com>
References: <CAH6Pt5om9-z_0ifofP=Gyfdkx+yrDirS9ysNUMxSk164sTsoaQ@mail.gmail.com>
 <CA+A4wOmOKPeA4vNLb-R-oG0MES=uCMM=Er72gPiUYB-P+Zm7nw@mail.gmail.com>
 <CAH6Pt5qVscEdWM=e7L55sr37jj10bY_NFPAAUav0nyHTb=rb=Q@mail.gmail.com>
 <CA+A4wOnTkUeQsvo_KcOHgEA103PCokLK9VdzqJ=AwaVG6zw=jA@mail.gmail.com>
Message-ID: <CAH6Pt5qTXq38TdRH9Y2WMqrbk2vr1y4+-EAWBoUhkhM=ceHJAA@mail.gmail.com>

Hi,

On Sat, Jul 10, 2021 at 5:09 PM Satrajit Ghosh <satra at mit.edu> wrote:
>
> hi mathew,
>
> categories are created by incf admins. in the past users were encouraged to tags and post everything under neuroquestions, as we did not want to blow up categories and everything could be searched through tags. for example:
>
> https://neurostars.org/tag/nibabel
>
> and here is an example of multi tag search.
>
> https://neurostars.org/search?q=tag%3Acifti%20tag%3Anibabel

Ah - yes - I get the idea, but that does make me wonder whether it
would be better to have a Discourse instance that was specific to
Python - equivalent to this mailing list, but with sub-topics.  I
really like the Jupyter setup where you go straight to various helpful
Categories, so it's pretty obvious where to start:

https://discourse.jupyter.org/

I can see that wouldn't make sense, for a site as general as
Neurostars - there would just be too many categories...

Cheers,

Matthew

From satra at mit.edu  Sat Jul 10 12:41:00 2021
From: satra at mit.edu (Satrajit Ghosh)
Date: Sat, 10 Jul 2021 12:41:00 -0400
Subject: [Neuroimaging] Discourse category for DICOM discussions
In-Reply-To: <CAH6Pt5qTXq38TdRH9Y2WMqrbk2vr1y4+-EAWBoUhkhM=ceHJAA@mail.gmail.com>
References: <CAH6Pt5om9-z_0ifofP=Gyfdkx+yrDirS9ysNUMxSk164sTsoaQ@mail.gmail.com>
 <CA+A4wOmOKPeA4vNLb-R-oG0MES=uCMM=Er72gPiUYB-P+Zm7nw@mail.gmail.com>
 <CAH6Pt5qVscEdWM=e7L55sr37jj10bY_NFPAAUav0nyHTb=rb=Q@mail.gmail.com>
 <CA+A4wOnTkUeQsvo_KcOHgEA103PCokLK9VdzqJ=AwaVG6zw=jA@mail.gmail.com>
 <CAH6Pt5qTXq38TdRH9Y2WMqrbk2vr1y4+-EAWBoUhkhM=ceHJAA@mail.gmail.com>
Message-ID: <CA+A4wOnBm_fGYSiba0bU6fsM+ShEggjQj86L8Wife1vSwRn9YQ@mail.gmail.com>

hi matthew,

i don't have a good answer to that other than it seems to have worked out
ok across the various python and other software tools discussed on
neurostars. perhaps the folks here could decide or we go with trying out
neurostars and seeing if we really run into those issues.

the other option for more specificity is to turn on discussions on the
github repo itself. that keeps it close to the code. here is an example of
trying to balance code, proximity, outreach, and community:
https://github.com/dandi/helpdesk/issues/new/choose

cheers,

satra

On Sat, Jul 10, 2021 at 12:30 PM Matthew Brett <matthew.brett at gmail.com>
wrote:

> Hi,
>
> On Sat, Jul 10, 2021 at 5:09 PM Satrajit Ghosh <satra at mit.edu> wrote:
> >
> > hi mathew,
> >
> > categories are created by incf admins. in the past users were encouraged
> to tags and post everything under neuroquestions, as we did not want to
> blow up categories and everything could be searched through tags. for
> example:
> >
> > https://neurostars.org/tag/nibabel
> >
> > and here is an example of multi tag search.
> >
> > https://neurostars.org/search?q=tag%3Acifti%20tag%3Anibabel
>
> Ah - yes - I get the idea, but that does make me wonder whether it
> would be better to have a Discourse instance that was specific to
> Python - equivalent to this mailing list, but with sub-topics.  I
> really like the Jupyter setup where you go straight to various helpful
> Categories, so it's pretty obvious where to start:
>
> https://discourse.jupyter.org/
>
> I can see that wouldn't make sense, for a site as general as
> Neurostars - there would just be too many categories...
>
> Cheers,
>
> Matthew
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From pieper at isomics.com  Sat Jul 10 12:46:02 2021
From: pieper at isomics.com (Steve Pieper)
Date: Sat, 10 Jul 2021 12:46:02 -0400
Subject: [Neuroimaging] Discourse category for DICOM discussions
In-Reply-To: <CAH6Pt5q+u0u2NdxbXAgxswaJ4pcBQ_GLCDLN=nCbO61hx8jqVw@mail.gmail.com>
References: <CAH6Pt5om9-z_0ifofP=Gyfdkx+yrDirS9ysNUMxSk164sTsoaQ@mail.gmail.com>
 <CA+A4wOmOKPeA4vNLb-R-oG0MES=uCMM=Er72gPiUYB-P+Zm7nw@mail.gmail.com>
 <CAH6Pt5qVscEdWM=e7L55sr37jj10bY_NFPAAUav0nyHTb=rb=Q@mail.gmail.com>
 <CADkb7uPRmO-ACh0OAkNnfjuq0sABJnw7xg8goynFWVwgK-67Ng@mail.gmail.com>
 <CAH6Pt5q+u0u2NdxbXAgxswaJ4pcBQ_GLCDLN=nCbO61hx8jqVw@mail.gmail.com>
Message-ID: <CADkb7uPjLDuLe69DVH96TSUXRhFd_fGAX-Vyi5csQBYQEFi-LA@mail.gmail.com>

Looks like some really great ideas and resources are coming together.  I'm
really glad to see you funded for this.

Folks may also be interested in highdicom:
https://github.com/MGHComputationalPathology/highdicom

It addresses objects like reports, parametric maps and segmentations that
could really be useful for neuroimaging.

We also have a lot of multimodality python dicom parsing code in Slicer
that would be nice to factor out.

Best,
Steve



On Sat, Jul 10, 2021 at 12:10 PM Matthew Brett <matthew.brett at gmail.com>
wrote:

> Hi Steve,
>
> Some sparse notes here:
>
>
> https://docs.google.com/document/d/1Ca999GAx1qfCT0Hw5JRlJSEJeVTRDYaIg1h1LWbgYoo/edit?usp=sharing
>
> The next plan was to have a show-and-tell session where we go over the
> main parts of the various Python libraries covering DICOM in
> neuroimaging, which we so far have as:
>
> dicom_parser
> dcmstack
> Nibabel/nicom
>
> All welcome, as usual; any other suggestions welcome.  We haven't got
> a time yet - I think Zvi had kindly agreed to poll and set that up
> next week.
>
> Cheers,
>
> Matthew
>
> On Sat, Jul 10, 2021 at 5:06 PM Steve Pieper <pieper at isomics.com> wrote:
> >
> > Hi Mathew and Satra -
> >
> > I'm sorry I couldn't attend the meeting yesterday, but I look forward to
> this further discussion.  Are there any notes from the meeting?
> >
> > Best,
> > Steve
> >
> > On Sat, Jul 10, 2021 at 11:54 AM Matthew Brett <matthew.brett at gmail.com>
> wrote:
> >>
> >> Hi,
> >>
> >> Ah - sorry - I didn't realize Neurostars was a Discourse instance - I
> >> hadn't looked for ages.  No, no reason, let's move there.  How do I
> >> create a new category?  Is there a system for collecting / archiving
> >> the post data so that we can replicate it if there's a problem?
> >>
> >> Cheers,
> >>
> >> Matthew
> >>
> >>
> >>
> >> On Sat, Jul 10, 2021 at 4:15 PM Satrajit Ghosh <satra at mit.edu> wrote:
> >> >
> >> > hi matthew,
> >> >
> >> > any reason not to use neurostars for this (which is a discourse
> platform)? a number of neuroimaging software discussions are already
> happening there, including questions about nibabel and dicom conversion
> tools.
> >> >
> >> > cheers,
> >> >
> >> > satra
> >> >
> >> > On Sat, Jul 10, 2021 at 10:43 AM Matthew Brett <
> matthew.brett at gmail.com> wrote:
> >> >>
> >> >> Hi,
> >> >>
> >> >> We had a good discussion yesterday about what to do next with Python
> and DICOM.
> >> >>
> >> >> To keep the discussion going, while not overloading your inboxes,
> I've
> >> >> asked Discourse for a Nipy Discourse instance, and I've made a
> >> >> category for the DICOM discussions, here:
> >> >>
> >> >> https://nipy.discourse.group/c/python-dicom
> >> >>
> >> >> Can I suggest that we move the DICOM discussions to that category?
> >> >> Then we can feed back here, from time to time.
> >> >>
> >> >> The Discourse category is all public, so you can always go and see
> >> >> what we are up to by following the link.  For those new to Discourse,
> >> >> it's a rather nice Forum-like system that has good email integration,
> >> >> and Markdown editing, so it's a nice way of making well-formed,
> >> >> publicly searchable messages and discussions, that you can use via
> >> >> email if you want.
> >> >>
> >> >> If anyone wants new categories or admin permissions on the Discourse
> >> >> instance, just let me know.
> >> >>
> >> >> Cheers,
> >> >>
> >> >> Matthew
> >> >> _______________________________________________
> >> >> Neuroimaging mailing list
> >> >> Neuroimaging at python.org
> >> >> https://mail.python.org/mailman/listinfo/neuroimaging
> >> >
> >> > _______________________________________________
> >> > Neuroimaging mailing list
> >> > Neuroimaging at python.org
> >> > https://mail.python.org/mailman/listinfo/neuroimaging
> >> _______________________________________________
> >> Neuroimaging mailing list
> >> Neuroimaging at python.org
> >> https://mail.python.org/mailman/listinfo/neuroimaging
> >
> > _______________________________________________
> > Neuroimaging mailing list
> > Neuroimaging at python.org
> > https://mail.python.org/mailman/listinfo/neuroimaging
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From matthew.brett at gmail.com  Sat Jul 10 12:56:01 2021
From: matthew.brett at gmail.com (Matthew Brett)
Date: Sat, 10 Jul 2021 17:56:01 +0100
Subject: [Neuroimaging] Discourse category for DICOM discussions
In-Reply-To: <CA+A4wOnBm_fGYSiba0bU6fsM+ShEggjQj86L8Wife1vSwRn9YQ@mail.gmail.com>
References: <CAH6Pt5om9-z_0ifofP=Gyfdkx+yrDirS9ysNUMxSk164sTsoaQ@mail.gmail.com>
 <CA+A4wOmOKPeA4vNLb-R-oG0MES=uCMM=Er72gPiUYB-P+Zm7nw@mail.gmail.com>
 <CAH6Pt5qVscEdWM=e7L55sr37jj10bY_NFPAAUav0nyHTb=rb=Q@mail.gmail.com>
 <CA+A4wOnTkUeQsvo_KcOHgEA103PCokLK9VdzqJ=AwaVG6zw=jA@mail.gmail.com>
 <CAH6Pt5qTXq38TdRH9Y2WMqrbk2vr1y4+-EAWBoUhkhM=ceHJAA@mail.gmail.com>
 <CA+A4wOnBm_fGYSiba0bU6fsM+ShEggjQj86L8Wife1vSwRn9YQ@mail.gmail.com>
Message-ID: <CAH6Pt5oruAJb_iuj=UeHhp8n1C+XKXMuGUfJXQPeHeGZnoX7Qg@mail.gmail.com>

Hi,

On Sat, Jul 10, 2021 at 5:41 PM Satrajit Ghosh <satra at mit.edu> wrote:
>
> hi matthew,
>
> i don't have a good answer to that other than it seems to have worked out ok across the various python and other software tools discussed on neurostars. perhaps the folks here could decide or we go with trying out neurostars and seeing if we really run into those issues.
>
> the other option for more specificity is to turn on discussions on the github repo itself. that keeps it close to the code. here is an example of trying to balance code, proximity, outreach, and community: https://github.com/dandi/helpdesk/issues/new/choose

Ah - I think that doesn't match our problem here - because we're
thinking about how to coordinate development across at least three
different projects, and therefore, repositories.

On reflection, I'd prefer to stick with the nipy.discourse.group DICOM
category, to have one place devoted to those discussions.   If it
looks like the discussions are getting more general than developing
DICOM conversion and APIs across the Python packages, then we can move
to Neurostars.

I don't see any need for this to compete with Neurostars - this is a
very specific developer discussion forum (to which, of course, anyone
is welcome), rather than the more general focus of Neurostars.

So - as you were - please do join us over at:

https://nipy.discourse.group/c/python-dicom

Cheers,

Matthew

From matthew.brett at gmail.com  Sat Jul 10 12:57:57 2021
From: matthew.brett at gmail.com (Matthew Brett)
Date: Sat, 10 Jul 2021 17:57:57 +0100
Subject: [Neuroimaging] Discourse category for DICOM discussions
In-Reply-To: <CADkb7uPjLDuLe69DVH96TSUXRhFd_fGAX-Vyi5csQBYQEFi-LA@mail.gmail.com>
References: <CAH6Pt5om9-z_0ifofP=Gyfdkx+yrDirS9ysNUMxSk164sTsoaQ@mail.gmail.com>
 <CA+A4wOmOKPeA4vNLb-R-oG0MES=uCMM=Er72gPiUYB-P+Zm7nw@mail.gmail.com>
 <CAH6Pt5qVscEdWM=e7L55sr37jj10bY_NFPAAUav0nyHTb=rb=Q@mail.gmail.com>
 <CADkb7uPRmO-ACh0OAkNnfjuq0sABJnw7xg8goynFWVwgK-67Ng@mail.gmail.com>
 <CAH6Pt5q+u0u2NdxbXAgxswaJ4pcBQ_GLCDLN=nCbO61hx8jqVw@mail.gmail.com>
 <CADkb7uPjLDuLe69DVH96TSUXRhFd_fGAX-Vyi5csQBYQEFi-LA@mail.gmail.com>
Message-ID: <CAH6Pt5p6dHu_Wnsnk36o_wkzOoGd8Mtd_HAOyPZA7HgcDjK+2Q@mail.gmail.com>

Hi Steve,

On Sat, Jul 10, 2021 at 5:46 PM Steve Pieper <pieper at isomics.com> wrote:
>
> Looks like some really great ideas and resources are coming together.  I'm really glad to see you funded for this.
>
> Folks may also be interested in highdicom: https://github.com/MGHComputationalPathology/highdicom
>
> It addresses objects like reports, parametric maps and segmentations that could really be useful for neuroimaging.
>
> We also have a lot of multimodality python dicom parsing code in Slicer that would be nice to factor out.

Wow - that does look very relevant and useful - thanks.  I wonder
whether you'd consider doing a show-and-tell for this stuff in the
next meeting?

Cheers,

Matthew

From pieper at isomics.com  Sat Jul 10 13:07:24 2021
From: pieper at isomics.com (Steve Pieper)
Date: Sat, 10 Jul 2021 13:07:24 -0400
Subject: [Neuroimaging] Discourse category for DICOM discussions
In-Reply-To: <CAH6Pt5p6dHu_Wnsnk36o_wkzOoGd8Mtd_HAOyPZA7HgcDjK+2Q@mail.gmail.com>
References: <CAH6Pt5om9-z_0ifofP=Gyfdkx+yrDirS9ysNUMxSk164sTsoaQ@mail.gmail.com>
 <CA+A4wOmOKPeA4vNLb-R-oG0MES=uCMM=Er72gPiUYB-P+Zm7nw@mail.gmail.com>
 <CAH6Pt5qVscEdWM=e7L55sr37jj10bY_NFPAAUav0nyHTb=rb=Q@mail.gmail.com>
 <CADkb7uPRmO-ACh0OAkNnfjuq0sABJnw7xg8goynFWVwgK-67Ng@mail.gmail.com>
 <CAH6Pt5q+u0u2NdxbXAgxswaJ4pcBQ_GLCDLN=nCbO61hx8jqVw@mail.gmail.com>
 <CADkb7uPjLDuLe69DVH96TSUXRhFd_fGAX-Vyi5csQBYQEFi-LA@mail.gmail.com>
 <CAH6Pt5p6dHu_Wnsnk36o_wkzOoGd8Mtd_HAOyPZA7HgcDjK+2Q@mail.gmail.com>
Message-ID: <CADkb7uNfjibeyPuxhr-GfGz7oM0Bg3uwiMBpBzu=zx+pZT8-dA@mail.gmail.com>

Hi Mathew -

Yes, would love to!

-Steve

On Sat, Jul 10, 2021 at 12:58 PM Matthew Brett <matthew.brett at gmail.com>
wrote:

> Hi Steve,
>
> On Sat, Jul 10, 2021 at 5:46 PM Steve Pieper <pieper at isomics.com> wrote:
> >
> > Looks like some really great ideas and resources are coming together.
> I'm really glad to see you funded for this.
> >
> > Folks may also be interested in highdicom:
> https://github.com/MGHComputationalPathology/highdicom
> >
> > It addresses objects like reports, parametric maps and segmentations
> that could really be useful for neuroimaging.
> >
> > We also have a lot of multimodality python dicom parsing code in Slicer
> that would be nice to factor out.
>
> Wow - that does look very relevant and useful - thanks.  I wonder
> whether you'd consider doing a show-and-tell for this stuff in the
> next meeting?
>
> Cheers,
>
> Matthew
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From satra at mit.edu  Sat Jul 10 13:18:57 2021
From: satra at mit.edu (Satrajit Ghosh)
Date: Sat, 10 Jul 2021 13:18:57 -0400
Subject: [Neuroimaging] Discourse category for DICOM discussions
In-Reply-To: <CAH6Pt5oruAJb_iuj=UeHhp8n1C+XKXMuGUfJXQPeHeGZnoX7Qg@mail.gmail.com>
References: <CAH6Pt5om9-z_0ifofP=Gyfdkx+yrDirS9ysNUMxSk164sTsoaQ@mail.gmail.com>
 <CA+A4wOmOKPeA4vNLb-R-oG0MES=uCMM=Er72gPiUYB-P+Zm7nw@mail.gmail.com>
 <CAH6Pt5qVscEdWM=e7L55sr37jj10bY_NFPAAUav0nyHTb=rb=Q@mail.gmail.com>
 <CA+A4wOnTkUeQsvo_KcOHgEA103PCokLK9VdzqJ=AwaVG6zw=jA@mail.gmail.com>
 <CAH6Pt5qTXq38TdRH9Y2WMqrbk2vr1y4+-EAWBoUhkhM=ceHJAA@mail.gmail.com>
 <CA+A4wOnBm_fGYSiba0bU6fsM+ShEggjQj86L8Wife1vSwRn9YQ@mail.gmail.com>
 <CAH6Pt5oruAJb_iuj=UeHhp8n1C+XKXMuGUfJXQPeHeGZnoX7Qg@mail.gmail.com>
Message-ID: <CA+A4wO=URMVmj0j37s=ysZsYgQQs7K0F48W8uKDU+4D+=zAdCg@mail.gmail.com>

hi matthew,

sounds good.

cheers,

satra

On Sat, Jul 10, 2021 at 12:56 PM Matthew Brett <matthew.brett at gmail.com>
wrote:

> Hi,
>
> On Sat, Jul 10, 2021 at 5:41 PM Satrajit Ghosh <satra at mit.edu> wrote:
> >
> > hi matthew,
> >
> > i don't have a good answer to that other than it seems to have worked
> out ok across the various python and other software tools discussed on
> neurostars. perhaps the folks here could decide or we go with trying out
> neurostars and seeing if we really run into those issues.
> >
> > the other option for more specificity is to turn on discussions on the
> github repo itself. that keeps it close to the code. here is an example of
> trying to balance code, proximity, outreach, and community:
> https://github.com/dandi/helpdesk/issues/new/choose
>
> Ah - I think that doesn't match our problem here - because we're
> thinking about how to coordinate development across at least three
> different projects, and therefore, repositories.
>
> On reflection, I'd prefer to stick with the nipy.discourse.group DICOM
> category, to have one place devoted to those discussions.   If it
> looks like the discussions are getting more general than developing
> DICOM conversion and APIs across the Python packages, then we can move
> to Neurostars.
>
> I don't see any need for this to compete with Neurostars - this is a
> very specific developer discussion forum (to which, of course, anyone
> is welcome), rather than the more general focus of Neurostars.
>
> So - as you were - please do join us over at:
>
> https://nipy.discourse.group/c/python-dicom
>
> Cheers,
>
> Matthew
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From z.baratz at gmail.com  Sat Jul 10 14:02:06 2021
From: z.baratz at gmail.com (Zvi Baratz)
Date: Sat, 10 Jul 2021 21:02:06 +0300
Subject: [Neuroimaging] Discourse category for DICOM discussions
In-Reply-To: <CA+A4wO=URMVmj0j37s=ysZsYgQQs7K0F48W8uKDU+4D+=zAdCg@mail.gmail.com>
References: <CAH6Pt5om9-z_0ifofP=Gyfdkx+yrDirS9ysNUMxSk164sTsoaQ@mail.gmail.com>
 <CA+A4wOmOKPeA4vNLb-R-oG0MES=uCMM=Er72gPiUYB-P+Zm7nw@mail.gmail.com>
 <CAH6Pt5qVscEdWM=e7L55sr37jj10bY_NFPAAUav0nyHTb=rb=Q@mail.gmail.com>
 <CA+A4wOnTkUeQsvo_KcOHgEA103PCokLK9VdzqJ=AwaVG6zw=jA@mail.gmail.com>
 <CAH6Pt5qTXq38TdRH9Y2WMqrbk2vr1y4+-EAWBoUhkhM=ceHJAA@mail.gmail.com>
 <CA+A4wOnBm_fGYSiba0bU6fsM+ShEggjQj86L8Wife1vSwRn9YQ@mail.gmail.com>
 <CAH6Pt5oruAJb_iuj=UeHhp8n1C+XKXMuGUfJXQPeHeGZnoX7Qg@mail.gmail.com>
 <CA+A4wO=URMVmj0j37s=ysZsYgQQs7K0F48W8uKDU+4D+=zAdCg@mail.gmail.com>
Message-ID: <CANJsFRa2zjef497QwzyUVvOikmJC7fo8MhNENBx=XnYLZB_stw@mail.gmail.com>

Hi,

Apologies for the delay, please fill in your preferences for the next
meeting at this Doodle
<https://doodle.com/poll/ba2xf5f5dddpchmb?utm_source=poll&utm_medium=link>
poll.
As Matthew suggested, this will be a "show-and-tell" in which the lead
maintainers of NiBabel, dcmstack, highdicom, and dicom_parser (myself) will
give a quick demo and/or guided tour of the codebase.
I think very exciting things are ahead - collaborating and integrating the
functionalities of these packages together could significantly enhance many
researchers' ability to access, share, and study large-scale DICOM archives.

Looking forward!
Zvi

On Sat, Jul 10, 2021 at 8:19 PM Satrajit Ghosh <satra at mit.edu> wrote:

> hi matthew,
>
> sounds good.
>
> cheers,
>
> satra
>
> On Sat, Jul 10, 2021 at 12:56 PM Matthew Brett <matthew.brett at gmail.com>
> wrote:
>
>> Hi,
>>
>> On Sat, Jul 10, 2021 at 5:41 PM Satrajit Ghosh <satra at mit.edu> wrote:
>> >
>> > hi matthew,
>> >
>> > i don't have a good answer to that other than it seems to have worked
>> out ok across the various python and other software tools discussed on
>> neurostars. perhaps the folks here could decide or we go with trying out
>> neurostars and seeing if we really run into those issues.
>> >
>> > the other option for more specificity is to turn on discussions on the
>> github repo itself. that keeps it close to the code. here is an example of
>> trying to balance code, proximity, outreach, and community:
>> https://github.com/dandi/helpdesk/issues/new/choose
>>
>> Ah - I think that doesn't match our problem here - because we're
>> thinking about how to coordinate development across at least three
>> different projects, and therefore, repositories.
>>
>> On reflection, I'd prefer to stick with the nipy.discourse.group DICOM
>> category, to have one place devoted to those discussions.   If it
>> looks like the discussions are getting more general than developing
>> DICOM conversion and APIs across the Python packages, then we can move
>> to Neurostars.
>>
>> I don't see any need for this to compete with Neurostars - this is a
>> very specific developer discussion forum (to which, of course, anyone
>> is welcome), rather than the more general focus of Neurostars.
>>
>> So - as you were - please do join us over at:
>>
>> https://nipy.discourse.group/c/python-dicom
>>
>> Cheers,
>>
>> Matthew
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From matthew.brett at gmail.com  Sat Jul 10 14:05:25 2021
From: matthew.brett at gmail.com (Matthew Brett)
Date: Sat, 10 Jul 2021 19:05:25 +0100
Subject: [Neuroimaging] Discourse category for DICOM discussions
In-Reply-To: <CA+A4wO=URMVmj0j37s=ysZsYgQQs7K0F48W8uKDU+4D+=zAdCg@mail.gmail.com>
References: <CAH6Pt5om9-z_0ifofP=Gyfdkx+yrDirS9ysNUMxSk164sTsoaQ@mail.gmail.com>
 <CA+A4wOmOKPeA4vNLb-R-oG0MES=uCMM=Er72gPiUYB-P+Zm7nw@mail.gmail.com>
 <CAH6Pt5qVscEdWM=e7L55sr37jj10bY_NFPAAUav0nyHTb=rb=Q@mail.gmail.com>
 <CA+A4wOnTkUeQsvo_KcOHgEA103PCokLK9VdzqJ=AwaVG6zw=jA@mail.gmail.com>
 <CAH6Pt5qTXq38TdRH9Y2WMqrbk2vr1y4+-EAWBoUhkhM=ceHJAA@mail.gmail.com>
 <CA+A4wOnBm_fGYSiba0bU6fsM+ShEggjQj86L8Wife1vSwRn9YQ@mail.gmail.com>
 <CAH6Pt5oruAJb_iuj=UeHhp8n1C+XKXMuGUfJXQPeHeGZnoX7Qg@mail.gmail.com>
 <CA+A4wO=URMVmj0j37s=ysZsYgQQs7K0F48W8uKDU+4D+=zAdCg@mail.gmail.com>
Message-ID: <CAH6Pt5ricAXq2CCAPD+46OTr6F5iU_pzzYzMFTtsb0f8w5Z1HA@mail.gmail.com>

Hi,

I put a specific bit in the welcome post for the Nipy Discourse site,
suggesting that people with questions on how to use packages go to
Neurostars instead:

https://nipy.discourse.group/t/welcome-to-the-nipy-discourse-instance/7

Cheers,

Matthew

On Sat, Jul 10, 2021 at 6:19 PM Satrajit Ghosh <satra at mit.edu> wrote:
>
> hi matthew,
>
> sounds good.
>
> cheers,
>
> satra
>
> On Sat, Jul 10, 2021 at 12:56 PM Matthew Brett <matthew.brett at gmail.com> wrote:
>>
>> Hi,
>>
>> On Sat, Jul 10, 2021 at 5:41 PM Satrajit Ghosh <satra at mit.edu> wrote:
>> >
>> > hi matthew,
>> >
>> > i don't have a good answer to that other than it seems to have worked out ok across the various python and other software tools discussed on neurostars. perhaps the folks here could decide or we go with trying out neurostars and seeing if we really run into those issues.
>> >
>> > the other option for more specificity is to turn on discussions on the github repo itself. that keeps it close to the code. here is an example of trying to balance code, proximity, outreach, and community: https://github.com/dandi/helpdesk/issues/new/choose
>>
>> Ah - I think that doesn't match our problem here - because we're
>> thinking about how to coordinate development across at least three
>> different projects, and therefore, repositories.
>>
>> On reflection, I'd prefer to stick with the nipy.discourse.group DICOM
>> category, to have one place devoted to those discussions.   If it
>> looks like the discussions are getting more general than developing
>> DICOM conversion and APIs across the Python packages, then we can move
>> to Neurostars.
>>
>> I don't see any need for this to compete with Neurostars - this is a
>> very specific developer discussion forum (to which, of course, anyone
>> is welcome), rather than the more general focus of Neurostars.
>>
>> So - as you were - please do join us over at:
>>
>> https://nipy.discourse.group/c/python-dicom
>>
>> Cheers,
>>
>> Matthew
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging

From reynoldr at mail.nih.gov  Mon Jul 12 11:05:11 2021
From: reynoldr at mail.nih.gov (Reynolds, Richard C. (NIH/NIMH) [E])
Date: Mon, 12 Jul 2021 15:05:11 +0000
Subject: [Neuroimaging] why 2 affine transforms in the nifti
In-Reply-To: <8a130e8d-aae6-6d05-734f-88f7b9901e34@upmc.fr>
References: <f54c4737-fc1e-f489-2056-300c9a1b86d5@upmc.fr>
 <2DE747CA-C241-46BA-BCD2-5D7BE11B3ABB@inria.fr>,
 <8a130e8d-aae6-6d05-734f-88f7b9901e34@upmc.fr>
Message-ID: <BLAPR09MB73958E904028A2289E216CD9F7159@BLAPR09MB7395.namprd09.prod.outlook.com>

Hi Romain,


As Demian mentions, having the 2 transforms allows one to have a dataset in both original space and standard space, for example.  The main package to use this is SPM, I believe, which might repeatedly modify the sform to get the volume into standard space without altering the data, thus without repeatedly interpolating and therefore blurring the data.  There was also an advantage of not having to even store the transformed result unless needed, possibly saving disk space.  I don't know that anyone takes advantage of that anymore.


Also, note that the qform and sform are not quite interchangeable.  The qform transformation is not a general affine, while the sform is.


At this point most people are using non-linear registration, which cannot be done through a simple affine, and so the qform/sform distinction might no longer be needed.


Most packages write out transformations separately so that they can be concatenated without repeated resampling/blurring of the volumetric data.  In AFNI, the sform and qform are just ijk to xyz transformations to put the data on a regular grid.  As mentioned, registration transformations are generally kept separate to be concatenated and applied.  So the sform and qform are always identical after a typical operation, as you mention.


If the qform and sform are different after the SPM registration, perhaps that registration transformation was not applied, in which case you might want to extract it into a text file.  Note that since it is presumably ijk-to-xyz, the sform cannot simply be applied on top of the qform.  It might be good to verify with the SPM folks how to properly extract the registration transformation, such as by multiplying the sform by the inverse of the qform.  The order would be important.


- rick

________________________________
From: VRomain <romain.valabregue at upmc.fr>
Sent: Friday, July 9, 2021 7:06 AM
To: neuroimaging at python.org <neuroimaging at python.org>
Subject: Re: [Neuroimaging] why 2 affine transforms in the nifti


Yes thanks for the reference, that is indeed the right place to start,

so ok it is recommended to use qform for the "subject space", and the sform for "standard space" but note that this is set by the [sq]form_code  and nothing prevent you to do the opposite of the recommendation with sform_code=1 and qform_code=2 for instance.

the doc, say you may need the both depending on the use case, but no way to know which one to use if both [sq]form_code are >0 (ok it is depending on the use case ...)


Just as an example of inconsistency, when you convert from dicom to nifti, you usually get both sform and qform set, with [sq]form_code to 1. but if you write an image with sitk, only the qform is set.


Many coregistration tools (fsl, freesurfer, ants, niftireg) make the choice to do not change the nifti header and to write the coregistration affine in a separate file, so for them, I do not see a need of 2 affines ... (this is the best choice to avoid any confusion, and then you can have as many registration to as many template you wish !)


Only spm (as far as I know), decide to change the nifti header after a coregistration. It has the advantage, that they then do not need to compose affine and non-linear registration (you can directly apply the non-linear field, because thanks to the header change, the affine registration is already applied) ... but even for that there is no need of 2 transform: (they could also change the affine, if there was only one in the header !)

is there any tools or use case, that need this 2 transforms ?


May be I am concern because I made the wrong choice to use spm coregister at the first place (old habit take time to change ...). When I mixt with other tools for other task, I may end up having problems ...

if you stay with other coregistration tool, you just do not care and stay with 2 identical affine stored in the header ...



Le 09/07/2021 ? 11:13, Demian Wassermann a ?crit :

Dear Romain,

I think that you refer to the qform and sform transforms. If I?m not wrong the main idea of storing these two transforms is that qform transforms between voxel space and subject space in mm, and that sform transforms between voxel space and a ?standard space? such as ACPC, or talairach (see https://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html ) so you?d encode the output of a linear registration towards such standard space. Then there is of course the issue of poor documentation and then the way the data is used despite the standard?s intent

Best
Demian
--
Demian Wassermann, PhD, HdR
demian.wassermann at inria.fr<mailto:demian.wassermann at inria.fr>
Associate Research Professor (CRCN)
Parietal Team
INRIA Saclay Ile-de-France
1 Rue Honor? d'Estienne d'Orves, 91120 Palaiseau





On 9 Jul 2021, at 10:51, VRomain <romain.valabregue at upmc.fr><mailto:romain.valabregue at upmc.fr> wrote:

Hello


As suggest by oscar I open a new thread, since there may be nothing to do with Nibabel CZI grant


So to resume, I sometimes get  troubles when playing with different software, because of the 2 affines stored in the nifti file.

(some software thing one should only read / write the sform, other the qform, so it is easy to get to inconsistency, that will just scratch your results)

Thanks @ oscar to point out the nitransforms repo - https://github.com/poldracklab/nitransforms <https://github.com/poldracklab/nitransforms><https://github.com/poldracklab/nitransforms>)

I'll have a closer look, this is indeed an important objectiv


I am curious, to know why it was a clever idea to store 2 affine ? ( I probably miss the point ... )

>From what I understand, it was meant to get an history of the registration made on the data. The only software I know that use it, is spm coregister function. they update the sform and keep the qform. Ok we can come back, but if for any reason one have to coregister a second time, then the information is lost (because they chose to update the sform, and the qform take the old sform value ...)

_______________________________________________
Neuroimaging mailing list
Neuroimaging at python.org<mailto:Neuroimaging at python.org>
https://mail.python.org/mailman/listinfo/neuroimaging







_______________________________________________
Neuroimaging mailing list
Neuroimaging at python.org<mailto:Neuroimaging at python.org>
https://mail.python.org/mailman/listinfo/neuroimaging

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From romain.valabregue at upmc.fr  Mon Jul 12 12:07:52 2021
From: romain.valabregue at upmc.fr (VRomain)
Date: Mon, 12 Jul 2021 18:07:52 +0200
Subject: [Neuroimaging] why 2 affine transforms in the nifti
In-Reply-To: <BLAPR09MB73958E904028A2289E216CD9F7159@BLAPR09MB7395.namprd09.prod.outlook.com>
References: <f54c4737-fc1e-f489-2056-300c9a1b86d5@upmc.fr>
 <2DE747CA-C241-46BA-BCD2-5D7BE11B3ABB@inria.fr>
 <8a130e8d-aae6-6d05-734f-88f7b9901e34@upmc.fr>
 <BLAPR09MB73958E904028A2289E216CD9F7159@BLAPR09MB7395.namprd09.prod.outlook.com>
Message-ID: <032045f4-67df-88f1-a2df-c746d26f63b7@upmc.fr>

Hello


thanks for sharing,


There is a bit of confusion here, because there are 2 distinct notions 
(that interacts)


1_ the fact to change the nifti header after an affine coregistraiton:

 ??? this is the spm way against all other coregistration software. The 
main advantage of changing the nifti header is that you can visualize 
the result of your registration without the need to interpolate (no 
resampling of the data). This is of minor importance since at the end 
usually you spatially normalize your data and other software combine the 
affine and the non linear transformation in order to have only one 
resampling. (so both way are equivalent)



2_ The fact to have 2 affine store in the nifti volume.


My point is that

 ??? _ I do not see,? any good reason to do this, because at the end you 
want to have one and only one affine associate to your volume

 ??? _ if sform and qform are alway the same ... what the point to store 
2 affine ?

 ??? _ if they can be different, which one to choose (The initial nifti 
definition is not clear about it)



@rick after a SPM coregistration you end up with 2 different affine, but 
this is not meant to be combine (the qform store the original affine and 
the sform the new affine (after registration)).? So there is no need of 
combination


My experience is that I can have serious problem when I have 2 different 
sform/qform, so the best after SPM coregister is to use fsl 
copysform2qform utility




I think that the best solution would be to remove one of the two affine 
in the nifti header, so that there can not be any ambiguity, but I guess 
there will be too much backard incompatibilities? ... So may be having 
sform and qform coding for the same affine is the best way to go.? But 
then it should be more advertise, so that this is the default when 
writing nifti


But ok : one can live with imperfect nifti definition ...? (




On 12/07/2021 17:05, Reynolds, Richard C. (NIH/NIMH) [E] via 
Neuroimaging wrote:
>
> Hi Romain,
>
>
> As Demian mentions, having the 2 transforms allows one to have a 
> dataset in both original space and standard space, for example.The 
> main package to use this is SPM, I believe, which might repeatedly 
> modify the sform to get the volume into standard space without 
> altering the data, thus without repeatedly interpolating and therefore 
> blurring the data.There was also an advantage of not having to even 
> store the transformed result unless needed, possibly saving disk 
> space.I don't know that anyone takes advantage of that anymore.
>
>
> Also, note that the qform and sform are not quite interchangeable.The 
> qform transformation is not a general affine, while the sform is.
>
>
> At this point most people are using non-linear registration, which 
> cannot be done through a simple affine, and so the qform/sform 
> distinction might no longer?be needed.
>
>
> Most packages write out transformations separately so that they can be 
> concatenated without repeated resampling/blurring of the volumetric 
> data.In AFNI, the sform and qform are just ijk to xyz transformations 
> to put the data on a regular grid.As mentioned, registration 
> transformations are generally kept separate to be concatenated and 
> applied.So the sform and qform are always identical after a typical 
> operation, as you mention.
>
>
> If the qform and sform are different after the SPM registration, 
> perhaps that registration?transformation was not applied, in which 
> case you might want to extract?it into a text file.Note that since it 
> is presumably ijk-to-xyz, the sform cannot simply be applied on top of 
> the qform.? It might be good to verify with the SPM folks how to 
> properly extract the registration transformation, such as by 
> multiplying the sform by the inverse of the qform.? The order would be 
> important.
>
>
> - rick
>
>
> ------------------------------------------------------------------------
> *From:* VRomain <romain.valabregue at upmc.fr>
> *Sent:* Friday, July 9, 2021 7:06 AM
> *To:* neuroimaging at python.org <neuroimaging at python.org>
> *Subject:* Re: [Neuroimaging] why 2 affine transforms in the nifti
>
> Yes thanks for the reference, that is indeed the right place to start,
>
> so ok it is recommended to use qform for the "subject space", and the 
> sform for "standard space" but note that this is set by the 
> [sq]form_code? and nothing prevent you to do the opposite of the 
> recommendation with sform_code=1 and qform_code=2 for instance.
>
> the doc, say you may need the both depending on the use case, but no 
> way to know which one to use if both [sq]form_code are >0 (ok it is 
> depending on the use case ...)
>
>
> Just as an example of inconsistency, when you convert from dicom to 
> nifti, you usually get both sform and qform set, with [sq]form_code to 
> 1. but if you write an image with sitk, only the qform is set.
>
>
> Many coregistration tools (fsl, freesurfer, ants, niftireg) make the 
> choice to do not change the nifti header and to write the 
> coregistration affine in a separate file, so for them, I do not see a 
> need of 2 affines ... (this is the best choice to avoid any confusion, 
> and then you can have as many registration to as many template you wish !)
>
>
> Only spm (as far as I know), decide to change the nifti header after a 
> coregistration. It has the advantage, that they then do not need to 
> compose affine and non-linear registration (you can directly apply the 
> non-linear field, because thanks to the header change, the affine 
> registration is already applied) ... but even for that there is no 
> need of 2 transform: (they could also change the affine, if there was 
> only one in the header !)
>
> is there any tools or use case, that need this 2 transforms ?
>
>
> May be I am concern because I made the wrong choice to use spm 
> coregister at the first place (old habit take time to change ...). 
> When I mixt with other tools for other task, I may end up having 
> problems ...
>
> if you stay with other coregistration tool, you just do not care and 
> stay with 2 identical affine stored in the header ...
>
>
>
>
> Le 09/07/2021 ? 11:13, Demian Wassermann a ?crit?:
>> Dear Romain,
>>
>> I think that you refer to the qform and sform transforms. If I?m not wrong the main idea of storing these two transforms is that qform transforms between voxel space and subject space in mm, and that sform transforms between voxel space and a ?standard space? such as ACPC, or talairach (seehttps://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html  ) so you?d encode the output of a linear registration towards such standard space. Then there is of course the issue of poor documentation and then the way the data is used despite the standard?s intent
>>
>> Best
>> Demian
>> --
>> Demian Wassermann, PhD, HdR
>> demian.wassermann at inria.fr  <mailto:demian.wassermann at inria.fr>
>> Associate Research Professor (CRCN)
>> Parietal Team
>> INRIA Saclay Ile-de-France
>> 1 Rue Honor? d'Estienne d'Orves, 91120 Palaiseau
>>
>>
>>
>>> On 9 Jul 2021, at 10:51, VRomain<romain.valabregue at upmc.fr>  <mailto:romain.valabregue at upmc.fr>  wrote:
>>>
>>> Hello
>>>
>>>
>>> As suggest by oscar I open a new thread, since there may be nothing to do with Nibabel CZI grant
>>>
>>>
>>> So to resume, I sometimes get  troubles when playing with different software, because of the 2 affines stored in the nifti file.
>>>
>>> (some software thing one should only read / write the sform, other the qform, so it is easy to get to inconsistency, that will just scratch your results)
>>>
>>> Thanks @ oscar to point out the nitransforms repo -https://github.com/poldracklab/nitransforms  <https://github.com/poldracklab/nitransforms>  <https://github.com/poldracklab/nitransforms>)
>>>
>>> I'll have a closer look, this is indeed an important objectiv
>>>
>>>
>>> I am curious, to know why it was a clever idea to store 2 affine ? ( I probably miss the point ... )
>>>
>>>  From what I understand, it was meant to get an history of the registration made on the data. The only software I know that use it, is spm coregister function. they update the sform and keep the qform. Ok we can come back, but if for any reason one have to coregister a second time, then the information is lost (because they chose to update the sform, and the qform take the old sform value ...)
>>>
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org  <mailto:Neuroimaging at python.org>
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org  <mailto:Neuroimaging at python.org>
>> https://mail.python.org/mailman/listinfo/neuroimaging
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
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From romain.valabregue at upmc.fr  Tue Jul 13 06:19:38 2021
From: romain.valabregue at upmc.fr (VRomain)
Date: Tue, 13 Jul 2021 12:19:38 +0200
Subject: [Neuroimaging] Discourse category for DICOM discussions
In-Reply-To: <CAH6Pt5q+u0u2NdxbXAgxswaJ4pcBQ_GLCDLN=nCbO61hx8jqVw@mail.gmail.com>
References: <CAH6Pt5om9-z_0ifofP=Gyfdkx+yrDirS9ysNUMxSk164sTsoaQ@mail.gmail.com>
 <CA+A4wOmOKPeA4vNLb-R-oG0MES=uCMM=Er72gPiUYB-P+Zm7nw@mail.gmail.com>
 <CAH6Pt5qVscEdWM=e7L55sr37jj10bY_NFPAAUav0nyHTb=rb=Q@mail.gmail.com>
 <CADkb7uPRmO-ACh0OAkNnfjuq0sABJnw7xg8goynFWVwgK-67Ng@mail.gmail.com>
 <CAH6Pt5q+u0u2NdxbXAgxswaJ4pcBQ_GLCDLN=nCbO61hx8jqVw@mail.gmail.com>
Message-ID: <1c90828f-34fa-cf16-974d-f86d75b236ee@upmc.fr>

Hi there


may be an other link worth to look at :

Julien which is not on this list ( lamy at unistra.fr ) have made nice 
development on dicom parsing

https://github.com/lamyj/odil/

and for conversion of Bruker raw data to dicom file (and then dicom to 
nifti)

and https://github.com/lamyj/dicomifier/


It is quite amazing to realize that Bruker, is not able to give us a 
decent dicom output, with all information one needs (like direction of 
diffusion, ...),

I was used to dcmstack, but for my bruker raw data, this is the tool to 
go ...


Romain



On 10/07/2021 18:09, Matthew Brett wrote:
> Hi Steve,
>
> Some sparse notes here:
>
> https://docs.google.com/document/d/1Ca999GAx1qfCT0Hw5JRlJSEJeVTRDYaIg1h1LWbgYoo/edit?usp=sharing
>
> The next plan was to have a show-and-tell session where we go over the
> main parts of the various Python libraries covering DICOM in
> neuroimaging, which we so far have as:
>
> dicom_parser
> dcmstack
> Nibabel/nicom
>
> All welcome, as usual; any other suggestions welcome.  We haven't got
> a time yet - I think Zvi had kindly agreed to poll and set that up
> next week.
>
> Cheers,
>
> Matthew
>
> On Sat, Jul 10, 2021 at 5:06 PM Steve Pieper <pieper at isomics.com> wrote:
>> Hi Mathew and Satra -
>>
>> I'm sorry I couldn't attend the meeting yesterday, but I look forward to this further discussion.  Are there any notes from the meeting?
>>
>> Best,
>> Steve
>>
>> On Sat, Jul 10, 2021 at 11:54 AM Matthew Brett <matthew.brett at gmail.com> wrote:
>>> Hi,
>>>
>>> Ah - sorry - I didn't realize Neurostars was a Discourse instance - I
>>> hadn't looked for ages.  No, no reason, let's move there.  How do I
>>> create a new category?  Is there a system for collecting / archiving
>>> the post data so that we can replicate it if there's a problem?
>>>
>>> Cheers,
>>>
>>> Matthew
>>>
>>>
>>>
>>> On Sat, Jul 10, 2021 at 4:15 PM Satrajit Ghosh <satra at mit.edu> wrote:
>>>> hi matthew,
>>>>
>>>> any reason not to use neurostars for this (which is a discourse platform)? a number of neuroimaging software discussions are already happening there, including questions about nibabel and dicom conversion tools.
>>>>
>>>> cheers,
>>>>
>>>> satra
>>>>
>>>> On Sat, Jul 10, 2021 at 10:43 AM Matthew Brett <matthew.brett at gmail.com> wrote:
>>>>> Hi,
>>>>>
>>>>> We had a good discussion yesterday about what to do next with Python and DICOM.
>>>>>
>>>>> To keep the discussion going, while not overloading your inboxes, I've
>>>>> asked Discourse for a Nipy Discourse instance, and I've made a
>>>>> category for the DICOM discussions, here:
>>>>>
>>>>> https://nipy.discourse.group/c/python-dicom
>>>>>
>>>>> Can I suggest that we move the DICOM discussions to that category?
>>>>> Then we can feed back here, from time to time.
>>>>>
>>>>> The Discourse category is all public, so you can always go and see
>>>>> what we are up to by following the link.  For those new to Discourse,
>>>>> it's a rather nice Forum-like system that has good email integration,
>>>>> and Markdown editing, so it's a nice way of making well-formed,
>>>>> publicly searchable messages and discussions, that you can use via
>>>>> email if you want.
>>>>>
>>>>> If anyone wants new categories or admin permissions on the Discourse
>>>>> instance, just let me know.
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Matthew
>>>>> _______________________________________________
>>>>> Neuroimaging mailing list
>>>>> Neuroimaging at python.org
>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>> _______________________________________________
>>>> Neuroimaging mailing list
>>>> Neuroimaging at python.org
>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging

From phd at oscaresteban.es  Tue Jul 13 08:57:52 2021
From: phd at oscaresteban.es (Oscar Esteban)
Date: Tue, 13 Jul 2021 14:57:52 +0200
Subject: [Neuroimaging] 3rd NiPreps/fMRIPrep roundup - tomorrow July 14
Message-ID: <CAAsFcgxpotN-NNnCtXM_9RjoWLTsq6YJHMTuti9r8QoORurgsQ@mail.gmail.com>

Hi all,

We will be having our bi-monthly roundup tomorrow July 14 @ 17.00 CEST.

If you want to know/keep updated about NiPreps (www.nipreps.org),
TemplateFlow (www.templateflow.org) and/or fMRIPrep (www.fmriprep.org),
please request joining our GH team (
https://github.com/orgs/nipreps/teams/fmriprep-contributors). The
announcement for tomorrow's gathering can be found here -
https://github.com/orgs/nipreps/teams/fmriprep-contributors/discussions/4

Looking forward to seeing you

Cheers,
Oscar
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From phd at oscaresteban.es  Wed Jul 14 09:23:21 2021
From: phd at oscaresteban.es (Oscar Esteban)
Date: Wed, 14 Jul 2021 15:23:21 +0200
Subject: [Neuroimaging] 3rd NiPreps/fMRIPrep roundup - tomorrow July 14
In-Reply-To: <CAAsFcgxpotN-NNnCtXM_9RjoWLTsq6YJHMTuti9r8QoORurgsQ@mail.gmail.com>
References: <CAAsFcgxpotN-NNnCtXM_9RjoWLTsq6YJHMTuti9r8QoORurgsQ@mail.gmail.com>
Message-ID: <CAAsFcgzB8SGbbOBBJ0CxY+n+9bUqn2b09EuQ=+E936WutYyrvQ@mail.gmail.com>

Hi all,

As Peer had already noticed on neurostars:

> Although I made the GH team public, it seems that you must belong in the
> organization to be able to see it.
>
> Anyone interested, please DM your GH username so that I add you to the
> team.
>
> For upcoming roundups, I?ll try to figure out a better way to go around
> this issue.
>

Sorry for the misunderstanding. See you later!

On Tue, Jul 13, 2021 at 2:57 PM Oscar Esteban <phd at oscaresteban.es> wrote:

> Hi all,
>
> We will be having our bi-monthly roundup tomorrow July 14 @ 17.00 CEST.
>
> If you want to know/keep updated about NiPreps (www.nipreps.org),
> TemplateFlow (www.templateflow.org) and/or fMRIPrep (www.fmriprep.org),
> please request joining our GH team (
> https://github.com/orgs/nipreps/teams/fmriprep-contributors). The
> announcement for tomorrow's gathering can be found here -
> https://github.com/orgs/nipreps/teams/fmriprep-contributors/discussions/4
>
> Looking forward to seeing you
>
> Cheers,
> Oscar
>
>
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From moloney at ohsu.edu  Fri Jul 16 14:13:05 2021
From: moloney at ohsu.edu (Brendan Moloney)
Date: Fri, 16 Jul 2021 18:13:05 +0000
Subject: [Neuroimaging] Discourse category for DICOM discussions
In-Reply-To: <1c90828f-34fa-cf16-974d-f86d75b236ee@upmc.fr>
References: <CAH6Pt5om9-z_0ifofP=Gyfdkx+yrDirS9ysNUMxSk164sTsoaQ@mail.gmail.com>
 <CA+A4wOmOKPeA4vNLb-R-oG0MES=uCMM=Er72gPiUYB-P+Zm7nw@mail.gmail.com>
 <CAH6Pt5qVscEdWM=e7L55sr37jj10bY_NFPAAUav0nyHTb=rb=Q@mail.gmail.com>
 <CADkb7uPRmO-ACh0OAkNnfjuq0sABJnw7xg8goynFWVwgK-67Ng@mail.gmail.com>
 <CAH6Pt5q+u0u2NdxbXAgxswaJ4pcBQ_GLCDLN=nCbO61hx8jqVw@mail.gmail.com>,
 <1c90828f-34fa-cf16-974d-f86d75b236ee@upmc.fr>
Message-ID: <25cd3c6345834d36aeffc73b50c0b4c2@ohsu.edu>

Hi,


Thanks for the tip for handling Bruker data.  We have been using a mix of home grown code and Bruker2Nifti.


Brendan Moloney
Senior Research Associate
Advanced Imaging Research Center
Oregon Health Science University
________________________________
From: Neuroimaging <neuroimaging-bounces+moloney=ohsu.edu at python.org> on behalf of VRomain <romain.valabregue at upmc.fr>
Sent: Tuesday, July 13, 2021 3:19:38 AM
To: neuroimaging at python.org
Cc: Julien Lamy
Subject: [EXTERNAL] Re: [Neuroimaging] Discourse category for DICOM discussions

Hi there


may be an other link worth to look at :

Julien which is not on this list ( lamy at unistra.fr ) have made nice
development on dicom parsing

https://github.com/lamyj/odil/

and for conversion of Bruker raw data to dicom file (and then dicom to
nifti)

and https://github.com/lamyj/dicomifier/


It is quite amazing to realize that Bruker, is not able to give us a
decent dicom output, with all information one needs (like direction of
diffusion, ...),

I was used to dcmstack, but for my bruker raw data, this is the tool to
go ...


Romain



On 10/07/2021 18:09, Matthew Brett wrote:
> Hi Steve,
>
> Some sparse notes here:
>
> https://docs.google.com/document/d/1Ca999GAx1qfCT0Hw5JRlJSEJeVTRDYaIg1h1LWbgYoo/edit?usp=sharing
>
> The next plan was to have a show-and-tell session where we go over the
> main parts of the various Python libraries covering DICOM in
> neuroimaging, which we so far have as:
>
> dicom_parser
> dcmstack
> Nibabel/nicom
>
> All welcome, as usual; any other suggestions welcome.  We haven't got
> a time yet - I think Zvi had kindly agreed to poll and set that up
> next week.
>
> Cheers,
>
> Matthew
>
> On Sat, Jul 10, 2021 at 5:06 PM Steve Pieper <pieper at isomics.com> wrote:
>> Hi Mathew and Satra -
>>
>> I'm sorry I couldn't attend the meeting yesterday, but I look forward to this further discussion.  Are there any notes from the meeting?
>>
>> Best,
>> Steve
>>
>> On Sat, Jul 10, 2021 at 11:54 AM Matthew Brett <matthew.brett at gmail.com> wrote:
>>> Hi,
>>>
>>> Ah - sorry - I didn't realize Neurostars was a Discourse instance - I
>>> hadn't looked for ages.  No, no reason, let's move there.  How do I
>>> create a new category?  Is there a system for collecting / archiving
>>> the post data so that we can replicate it if there's a problem?
>>>
>>> Cheers,
>>>
>>> Matthew
>>>
>>>
>>>
>>> On Sat, Jul 10, 2021 at 4:15 PM Satrajit Ghosh <satra at mit.edu> wrote:
>>>> hi matthew,
>>>>
>>>> any reason not to use neurostars for this (which is a discourse platform)? a number of neuroimaging software discussions are already happening there, including questions about nibabel and dicom conversion tools.
>>>>
>>>> cheers,
>>>>
>>>> satra
>>>>
>>>> On Sat, Jul 10, 2021 at 10:43 AM Matthew Brett <matthew.brett at gmail.com> wrote:
>>>>> Hi,
>>>>>
>>>>> We had a good discussion yesterday about what to do next with Python and DICOM.
>>>>>
>>>>> To keep the discussion going, while not overloading your inboxes, I've
>>>>> asked Discourse for a Nipy Discourse instance, and I've made a
>>>>> category for the DICOM discussions, here:
>>>>>
>>>>> https://nipy.discourse.group/c/python-dicom
>>>>>
>>>>> Can I suggest that we move the DICOM discussions to that category?
>>>>> Then we can feed back here, from time to time.
>>>>>
>>>>> The Discourse category is all public, so you can always go and see
>>>>> what we are up to by following the link.  For those new to Discourse,
>>>>> it's a rather nice Forum-like system that has good email integration,
>>>>> and Markdown editing, so it's a nice way of making well-formed,
>>>>> publicly searchable messages and discussions, that you can use via
>>>>> email if you want.
>>>>>
>>>>> If anyone wants new categories or admin permissions on the Discourse
>>>>> instance, just let me know.
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Matthew
>>>>> _______________________________________________
>>>>> Neuroimaging mailing list
>>>>> Neuroimaging at python.org
>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>> _______________________________________________
>>>> Neuroimaging mailing list
>>>> Neuroimaging at python.org
>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
_______________________________________________
Neuroimaging mailing list
Neuroimaging at python.org
https://mail.python.org/mailman/listinfo/neuroimaging
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From yuva2257 at gmail.com  Sun Jul 18 23:20:50 2021
From: yuva2257 at gmail.com (Yuvaraj Rajamanickam)
Date: Mon, 19 Jul 2021 11:20:50 +0800
Subject: [Neuroimaging] Call for Chapter for Springer Book by M. Murugappan
 and R. Yuvaraj (Editors)
Message-ID: <CAD3ZSf6cFFUbOwztTpzn-F=+RD9xNU3yMw0f6DVsGEie3t3mOw@mail.gmail.com>

Dear Researchers,


Good day to you. Currently, we are accepting the high-quality book chapters
for our upcoming edited book in *Springer,* titled, *Biomedical
signal-based computer-aided diagnosis for neurological disorders*. Please
see below for more information.

We invite you and your network connections to consider submitting a
high-quality paper related to the aim and scope of this book for possible
publication. If possible, you could share this CFP in your network for
their possible contribution. Please feel free to contact us, if you have
any questions.

Submission link: https://easychair.org/conferences/?conf=bscadnd2021

Any queries, please feel free to write to us at bookchapter.bscad at gmail.com and
CC to m.murugappan at kcst.edu.kw ; yuvaraj.rajamanickam at nie.edu.sg.


Major topics to be included in the book are:

?Introduction to neurological disorders (ND) and biomedical signal
processing.
?Basic principles of CAD in ND diagnosis.
?Characterization of biomedical signals in ND.
?Feature engineering and optimization.
?Machine learning techniques in CAD for ND
?Deep learning algorithms in CAD for ND
?Neural network applications in CAD for ND
?Fuzzy logic and optimization techniques
?Supervised and unsupervised learning
?Case studies related to ND diagnosis.
?Challenges in the CAD for ND
?Advances and trends in CAD for ND diagnosis.

?Open Challenges in CAD in ND diagnosis


Important dates

?Abstract Submission (max 250 words): 30th July 2021

?Acceptance of abstract: 5th August 2021

?Full chapter submission:15th September 2021

?Authors notification: 15th October 2021

?Camera ready submission: 10th November 2021

?Permission and copyright:20th November 2021

?Publication date: 1st quarter of 2022

Submission guidelines

?MS Word, single column, Times New Roman, 11 font size, 1.15 spacing.

?References must follow springer style.

?Length of the chapter: 20-25 pages (11550 words (approx.)) including
references, tables, figures.

?Similarity index should be less than 10 % (without reference).

?All figures must be supplied as final artwork (e.g., JPEG, PNG, TIFF,
etc.) at high-resolution.

NO PUBLICATION/ ARTICLE PROCESSING FEE.
?All manuscripts are accepted based on a double-blind peer review editorial
process.
Indexed by Web of Science (WoS), SCOPUS, Google Scholar, SCImago


Regards
YUVARAJ
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From garyfallidis at gmail.com  Thu Jul 22 13:12:17 2021
From: garyfallidis at gmail.com (Eleftherios Garyfallidis)
Date: Thu, 22 Jul 2021 13:12:17 -0400
Subject: [Neuroimaging] [DIPY] New educational course series available online
Message-ID: <CAN6JmWO=UAbDJ_QmnfeV_VtUUeafZXE8wa8_nOJ=BHKjo2W+oQ@mail.gmail.com>

Hi Everyone!

We are very happy to announce that  a new educational course series is
available online in our YouTube Channel
https://youtube.com/playlist?list=PLRZ9VSqV-6soOC0rUEAOV-QiSa_Qxk8JM

This is a complete course on Diffusion MRI with Theory and Practice (Code
or CLIs).

If you do like and use DIPY please do give us a star in GitHub and cite the
piece of software that you are using! It encourages us to keep going!

May your data live a new life!!
Best regards,
Eleftherios

p.s. Questions in relation to the videos can be asked in our Gitter channel
found here https://gitter.im/dipy/dipy
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From seralouk at hotmail.com  Thu Jul 22 16:54:57 2021
From: seralouk at hotmail.com (Serafeim Loukas)
Date: Thu, 22 Jul 2021 20:54:57 +0000
Subject: [Neuroimaging] [DIPY] New educational course series available
 online
In-Reply-To: <CAN6JmWO=UAbDJ_QmnfeV_VtUUeafZXE8wa8_nOJ=BHKjo2W+oQ@mail.gmail.com>
References: <CAN6JmWO=UAbDJ_QmnfeV_VtUUeafZXE8wa8_nOJ=BHKjo2W+oQ@mail.gmail.com>
Message-ID: <PA4PR04MB761651AC889BA6ACAFBF5915D7E49@PA4PR04MB7616.eurprd04.prod.outlook.com>

Amazing!
Keep up the amazing work.

Best,
Serafeim

On 22 Jul 2021, at 19:13, Eleftherios Garyfallidis <garyfallidis at gmail.com> wrote:

?
Hi Everyone!

We are very happy to announce that  a new educational course series is available online in our YouTube Channel
https://youtube.com/playlist?list=PLRZ9VSqV-6soOC0rUEAOV-QiSa_Qxk8JM

This is a complete course on Diffusion MRI with Theory and Practice (Code or CLIs).

If you do like and use DIPY please do give us a star in GitHub and cite the piece of software that you are using! It encourages us to keep going!

May your data live a new life!!
Best regards,
Eleftherios

p.s. Questions in relation to the videos can be asked in our Gitter channel found here https://gitter.im/dipy/dipy

_______________________________________________
Neuroimaging mailing list
Neuroimaging at python.org
https://mail.python.org/mailman/listinfo/neuroimaging
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From elef at indiana.edu  Thu Jul 22 18:06:34 2021
From: elef at indiana.edu (Eleftherios Garyfallidis)
Date: Thu, 22 Jul 2021 18:06:34 -0400
Subject: [Neuroimaging] [DIPY] New educational course series available
 online
In-Reply-To: <PA4PR04MB761651AC889BA6ACAFBF5915D7E49@PA4PR04MB7616.eurprd04.prod.outlook.com>
References: <CAN6JmWO=UAbDJ_QmnfeV_VtUUeafZXE8wa8_nOJ=BHKjo2W+oQ@mail.gmail.com>
 <PA4PR04MB761651AC889BA6ACAFBF5915D7E49@PA4PR04MB7616.eurprd04.prod.outlook.com>
Message-ID: <CAN6JmWPAUrhqd5de2SYiVssoL4WfwEMvxxQBhQWS4GiV=VrkAg@mail.gmail.com>

Thank you Serafeim.

On Thu, Jul 22, 2021 at 4:55 PM Serafeim Loukas <seralouk at hotmail.com>
wrote:

> Amazing!
> Keep up the amazing work.
>
> Best,
> Serafeim
>
> On 22 Jul 2021, at 19:13, Eleftherios Garyfallidis <garyfallidis at gmail.com>
> wrote:
>
> ?
> Hi Everyone!
>
> We are very happy to announce that  a new educational course series is
> available online in our YouTube Channel
> https://youtube.com/playlist?list=PLRZ9VSqV-6soOC0rUEAOV-QiSa_Qxk8JM
>
> This is a complete course on Diffusion MRI with Theory and Practice (Code
> or CLIs).
>
> If you do like and use DIPY please do give us a star in GitHub and cite
> the piece of software that you are using! It encourages us to keep going!
>
> May your data live a new life!!
> Best regards,
> Eleftherios
>
> p.s. Questions in relation to the videos can be asked in our Gitter
> channel found here https://gitter.im/dipy/dipy
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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