From samuel.garcia at cnrs.fr Tue Sep 4 10:38:43 2018
From: samuel.garcia at cnrs.fr (Samuel Garcia)
Date: Tue, 4 Sep 2018 16:38:43 +0200
Subject: [Neuroimaging] Spike sorting with tridesclous : release 1.0.0
Message-ID: <75e0eb58-7c83-398a-1487-17d7cfd0383c@cnrs.fr>
Dear all,
I'm pleased to announce the v1.0.0 release of tridesclous
.
This tools could interest researcher that use multi electrode cellular
electrophysiology recordings.
Tridesclous is a tool for *spike sorting* written in python.
Features:
* can be used *offline* with several formats (binary raw, blackrock,
neuralynx, plexon, tdt...)
* can be used *online* with pyacq with several hardware (NI, MCC,
blackrock, multichannel, ...)
* methods based on mix of "legacy clustering" + "template matching",
so it resolve spike collision
* well design user interface (UI) with multi view. This allow fast and
precise check of isolated neurons.
* 2 level for users : script or UI
* usable from several channel (tetrodes) to some hundreds of channels
(dense arrays)
* can use GPU (with opencl) for some step of processing, so it can be fast
* quick start guide with open data
* 100% open source
Doc: https://tridesclous.readthedocs.io/en/latest/
Code: https://github.com/tridesclous/tridesclous
Best,
Samuel
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
From keschenb at uw.edu Tue Sep 4 14:11:29 2018
From: keschenb at uw.edu (Kristian M Eschenburg)
Date: Tue, 4 Sep 2018 11:11:29 -0700
Subject: [Neuroimaging] using bedpostx diffusion model in dipy
Message-ID:
Hi All
Question -- does dipy support the use of the bedpostx diffusion model for
generating probabilistic tractography? I've run bedpostx on a large set of
diffusion images and am interested in using some of the tracking methods
contained in Dipy.
Thanks!
k
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
From alexandre.gramfort at inria.fr Tue Sep 4 14:57:43 2018
From: alexandre.gramfort at inria.fr (Alexandre Gramfort)
Date: Tue, 4 Sep 2018 20:57:43 +0200
Subject: [Neuroimaging] Spike sorting with tridesclous : release 1.0.0
In-Reply-To: <75e0eb58-7c83-398a-1487-17d7cfd0383c@cnrs.fr>
References: <75e0eb58-7c83-398a-1487-17d7cfd0383c@cnrs.fr>
Message-ID:
congrats Samuel !
Alex
On Tue, Sep 4, 2018 at 4:42 PM Samuel Garcia wrote:
> Dear all,
>
> I'm pleased to announce the v1.0.0 release of tridesclous
> .
>
> This tools could interest researcher that use multi electrode cellular
> electrophysiology recordings.
>
> Tridesclous is a tool for *spike sorting* written in python.
>
>
> Features:
>
> - can be used *offline* with several formats (binary raw, blackrock,
> neuralynx, plexon, tdt...)
> - can be used *online* with pyacq with several hardware (NI, MCC,
> blackrock, multichannel, ...)
> - methods based on mix of "legacy clustering" + "template matching",
> so it resolve spike collision
> - well design user interface (UI) with multi view. This allow fast and
> precise check of isolated neurons.
> - 2 level for users : script or UI
> - usable from several channel (tetrodes) to some hundreds of channels
> (dense arrays)
> - can use GPU (with opencl) for some step of processing, so it can be
> fast
> - quick start guide with open data
> - 100% open source
>
>
> Doc: https://tridesclous.readthedocs.io/en/latest/
>
> Code: https://github.com/tridesclous/tridesclous
>
>
> Best,
>
>
> Samuel
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
From elef at indiana.edu Tue Sep 4 19:48:03 2018
From: elef at indiana.edu (Eleftherios Garyfallidis)
Date: Tue, 4 Sep 2018 19:48:03 -0400
Subject: [Neuroimaging] using bedpostx diffusion model in dipy
In-Reply-To:
References:
Message-ID:
I do not think so. As far as I know we have never tried this. In theory
should be doable with a bit of code (or more than a bit).
On Tue, Sep 4, 2018 at 2:12 PM Kristian M Eschenburg
wrote:
> Hi All
>
> Question -- does dipy support the use of the bedpostx diffusion model for
> generating probabilistic tractography? I've run bedpostx on a large set of
> diffusion images and am interested in using some of the tracking methods
> contained in Dipy.
>
> Thanks!
>
>
> k
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
From matthew.brett at gmail.com Thu Sep 6 05:32:44 2018
From: matthew.brett at gmail.com (Matthew Brett)
Date: Thu, 6 Sep 2018 10:32:44 +0100
Subject: [Neuroimaging] Affine transformations
In-Reply-To:
References: <20180831145127.Horde.dEbME051yHvSIMhXHdsPte9@webmail.uni-jena.de>
Message-ID:
Oops,
On Fri, Aug 31, 2018 at 2:15 PM, Matthew Brett wrote:
[snip]
> I think you'll find that the center doesn't matter for the zooms
> because, if Z is a zooming affine, and hence of this form:
>
> Z = [[a, 0, 0, 0],
> [0, b, 0, 0],
> [0, 0, c, 0],
> [0, 0, 0, 1]]
>
> then Tinv.dot(Z).dot(T) == Z for any translations in T.
How silly of me. For some reason, as I woke up, I realized that's
obviously not true, and the zooms do change the translations, as would
have been obvious if I'd done the multiplication properly:
In [22]: import sympy as sy
In [23]: a, b, c, x, y, z = sy.symbols('a, b, c, x, y, z')
In [24]: T = Matrix([[1, 0, 0, x],
...: [0, 1, 0, y],
...: [0, 0, 1, z],
...: [0, 0, 0, 1]])
...:
In [25]: Z = Matrix([[a, 0, 0, 0],
...: [0, b, 0, 0],
...: [0, 0, c, 0],
...: [0, 0, 0, 1]])
...:
In [26]: T.inv() * Z * T
Out[26]:
Matrix([
[a, 0, 0, a*x - x],
[0, b, 0, b*y - y],
[0, 0, c, c*z - z],
[0, 0, 0, 1]])
So - yes - it does make a difference (to the origin) whether you zoom
after a translation, or not.
Sorry about that,
Cheers,
Matthew
From stefan.hoffmann at uni-jena.de Thu Sep 6 10:17:20 2018
From: stefan.hoffmann at uni-jena.de (Stefan Hoffmann)
Date: Thu, 06 Sep 2018 16:17:20 +0200
Subject: [Neuroimaging] Affine transformations
In-Reply-To:
References: <20180831145127.Horde.dEbME051yHvSIMhXHdsPte9@webmail.uni-jena.de>
Message-ID: <20180906161720.Horde.OJtpaZyxdOn_wSD38p78aPS@webmail.uni-jena.de>
No worries,
thanks for still caring after all this time.
And thanks for your help in first place!
best regards,
Stefan
Zitat von Matthew Brett :
> Oops,
>
> On Fri, Aug 31, 2018 at 2:15 PM, Matthew Brett
> wrote:
> [snip]
>> I think you'll find that the center doesn't matter for the zooms
>> because, if Z is a zooming affine, and hence of this form:
>>
>> Z = [[a, 0, 0, 0],
>> [0, b, 0, 0],
>> [0, 0, c, 0],
>> [0, 0, 0, 1]]
>>
>> then Tinv.dot(Z).dot(T) == Z for any translations in T.
>
> How silly of me. For some reason, as I woke up, I realized that's
> obviously not true, and the zooms do change the translations, as would
> have been obvious if I'd done the multiplication properly:
>
> In [22]: import sympy as sy
> In [23]: a, b, c, x, y, z = sy.symbols('a, b, c, x, y, z')
> In [24]: T = Matrix([[1, 0, 0, x],
> ...: [0, 1, 0, y],
> ...: [0, 0, 1, z],
> ...: [0, 0, 0, 1]])
> ...:
> In [25]: Z = Matrix([[a, 0, 0, 0],
> ...: [0, b, 0, 0],
> ...: [0, 0, c, 0],
> ...: [0, 0, 0, 1]])
> ...:
> In [26]: T.inv() * Z * T
> Out[26]:
> Matrix([
> [a, 0, 0, a*x - x],
> [0, b, 0, b*y - y],
> [0, 0, c, c*z - z],
> [0, 0, 0, 1]])
>
> So - yes - it does make a difference (to the origin) whether you zoom
> after a translation, or not.
>
> Sorry about that,
>
> Cheers,
>
> Matthew
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
From maxwell4444 at hotmail.com Fri Sep 7 09:40:52 2018
From: maxwell4444 at hotmail.com (Y X)
Date: Fri, 7 Sep 2018 13:40:52 +0000
Subject: [Neuroimaging] Question about DIPY MAP-MRI model
Message-ID:
Dear DIPY developer,
I am a user of DIPY and find MAP-MRI model is very useful. During my testing, I found a potential error here for non-gaussian (NG) parameter. The NG and NG perpendicular maps looks not correct as a low intensity was observed at WM area, and the NG parallel maps looks like a NG contrast.
Here the data I test is using a 2 shell DWI data (b 0, 1000, 2000, 64 dir each shell), a DSI data was also test with similar result with Q4 half setting.
I like the DIPY tools and MAP-MRI model here, can you help with the problem?
Bests,
Xu
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Figure_1.png
Type: image/png
Size: 103832 bytes
Desc: Figure_1.png
URL:
From fick.rutger at gmail.com Mon Sep 10 06:45:52 2018
From: fick.rutger at gmail.com (Rutger Fick)
Date: Mon, 10 Sep 2018 12:45:52 +0200
Subject: [Neuroimaging] Question about DIPY MAP-MRI model
In-Reply-To:
References:
Message-ID:
Hi Xu,
Can you make the plots with the corresponding colorbars next to them? It
will be easier to judge the values then.
Are you following the same steps as in the dipy mapmri example to generate
these plots?
Rutger
On Fri, 7 Sep 2018 at 15:42, Y X wrote:
> Dear DIPY developer,
>
> I am a user of DIPY and find MAP-MRI model is very useful. During my
> testing, I found a potential error here for non-gaussian (NG) parameter.
> The NG and NG perpendicular maps looks not correct as a low intensity was
> observed at WM area, and the NG parallel maps looks like a NG contrast.
>
>
>
> Here the data I test is using a 2 shell DWI data (b 0, 1000, 2000, 64 dir
> each shell), a DSI data was also test with similar result with Q4 half
> setting.
>
>
>
> I like the DIPY tools and MAP-MRI model here, can you help with the
> problem?
>
>
>
> Bests,
>
> Xu
>
>
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
From xzhen3 at wisc.edu Mon Sep 10 12:39:03 2018
From: xzhen3 at wisc.edu (Xingjian Zhen)
Date: Mon, 10 Sep 2018 11:39:03 -0500
Subject: [Neuroimaging] [DIPY] Do you have tools using DTI to track the
fibers?
Message-ID: <0C85D84B-57E6-4295-96AA-A33FC310C257@wisc.edu>
Hi dear officers,
Do you have tutorials about using DTI ( shape: m x n x p x 3 x 3 ) to trace the fibers with DIPY?
Thank you so much.
?
Best wishes.
Xingjian Zhen
Computer Science, UW-Madison
Medical Sciences Center,
University Ave,
Madison, WI 53706
xzhen3 at wisc.edu
+1(608)335-9054
From Kai.Wang-1 at Colorado.EDU Tue Sep 11 14:51:42 2018
From: Kai.Wang-1 at Colorado.EDU (Kai Wang)
Date: Tue, 11 Sep 2018 18:51:42 +0000
Subject: [Neuroimaging] [PySurfer] how to customize the colormap(LUT)?
Message-ID:
Dear PySurfer experts,
I'm trying to plot 17 masks (a parcellation) on the brain surfer. Not finding the pre-defined colormaps ideal, I would like to customize the colors. I only need one color for each mask, not a range of colors. Can I specify RGBA values to use for each mask?
Thank you very much,
Kai Wang, Ph.D.
Postdoctoral Research associate
Institute of Cognitive Science, University of Colorado Boulder
1777 Exposition Dr., Boulder, CO, 80301
kai.wang-1 at colorado.edu
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
From mwaskom at nyu.edu Tue Sep 11 15:01:02 2018
From: mwaskom at nyu.edu (Michael Waskom)
Date: Tue, 11 Sep 2018 15:01:02 -0400
Subject: [Neuroimaging] [PySurfer] how to customize the colormap(LUT)?
In-Reply-To:
References:
Message-ID:
Hi Kai,
`Brain.add_data` accepts a list or array of colors for the colormap
parameter:
http://pysurfer.github.io/generated/surfer.Brain.html#surfer.Brain.add_data
Best,
Michael
On Tue, Sep 11, 2018 at 2:51 PM, Kai Wang wrote:
> Dear PySurfer experts,
>
>
>
> I?m trying to plot 17 masks (a parcellation) on the brain surfer.
> Not finding the pre-defined colormaps ideal, I would like to customize the
> colors. I only need one color for each mask, not a range of colors. Can I
> specify RGBA values to use for each mask?
>
>
>
>
>
> Thank you very much,
>
> Kai Wang, Ph.D.
>
>
>
> Postdoctoral Research associate
>
> Institute of Cognitive Science, University of Colorado Boulder
>
> 1777 Exposition Dr., Boulder, CO, 80301
>
> kai.wang-1 at colorado.edu
>
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
From gabriele.arnulfo at gmail.com Wed Sep 12 04:27:22 2018
From: gabriele.arnulfo at gmail.com (Gabriele Arnulfo)
Date: Wed, 12 Sep 2018 10:27:22 +0200
Subject: [Neuroimaging] [PySurfer] how to customize the colormap(LUT)?
In-Reply-To:
References:
Message-ID:
Dear Kai Wang,
You can pass matplotlib colormaps to Brain command.
Il Mar 11 Set 2018, 20:51 Kai Wang ha scritto:
> Dear PySurfer experts,
>
>
>
> I?m trying to plot 17 masks (a parcellation) on the brain surfer.
> Not finding the pre-defined colormaps ideal, I would like to customize the
> colors. I only need one color for each mask, not a range of colors. Can I
> specify RGBA values to use for each mask?
>
>
>
>
>
> Thank you very much,
>
> Kai Wang, Ph.D.
>
>
>
> Postdoctoral Research associate
>
> Institute of Cognitive Science, University of Colorado Boulder
>
> 1777 Exposition Dr., Boulder, CO, 80301
>
> kai.wang-1 at colorado.edu
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
From anders.eklund at liu.se Sat Sep 15 07:25:30 2018
From: anders.eklund at liu.se (Anders Eklund)
Date: Sat, 15 Sep 2018 11:25:30 +0000
Subject: [Neuroimaging] =?iso-8859-1?q?Postdoc_position_in_deep_learning_?=
=?iso-8859-1?q?at_Link=F6ping_University=2C_Sweden?=
Message-ID:
Hello,
I'm looking for a postdoc to work on medical image processing and deep learning of neuroimaging data (structural MRI, diffusion MRI (especially q-space trajectory imaging, QTI) and functional MRI). I'm looking for someone with experience in CNNs (convolutional neural networks) and GANs (generative adversarial networks), or someone who has a strong interest in data analysis and deep learning.
Starting salary (before tax) is approximately 3500 EUR at the current EUR / SEK exchange rate. The position is for 2 years, and can be extended for 1 more year.
For more information, see (apply through the ad)
https://liu.se/en/work-at-liu/vacancies?rmpage=job&rmjob=9259&rmlang=UK
- Anders
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
From jingweili.sjtu.nus at gmail.com Tue Sep 18 04:07:32 2018
From: jingweili.sjtu.nus at gmail.com (Jingwei Li)
Date: Tue, 18 Sep 2018 16:07:32 +0800
Subject: [Neuroimaging] [fmriprep] Pick middle point of ribbon
Message-ID:
Dear fmriprep experts,
I found that when fmriprep does projection from EPI to fsaverage space, it
equally samples 6 points between pial surface and white-matter surface and
averages them. If I want to only pick the middle point of the ribbon, is
there a way to modify fmriprep code to achieve this? Thanks!
Regards,
Jingwei
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
From markiewicz at stanford.edu Tue Sep 18 08:47:12 2018
From: markiewicz at stanford.edu (Christopher Markiewicz)
Date: Tue, 18 Sep 2018 12:47:12 +0000
Subject: [Neuroimaging] [fmriprep] Pick middle point of ribbon
In-Reply-To:
References:
Message-ID:
Hi Jingwei,
To keep the number of channels constrained, fMRIPrep support is offered on Neurostars [0] and the GitHub issues page [1].
Best,
Chris
[0] https://neurostars.org/tags/fmriprep
[1] https://github.com/poldracklab/fmriprep/issues/
________________________________
From: Neuroimaging on behalf of Jingwei Li
Sent: Tuesday, September 18, 2018 4:07:32 AM
To: neuroimaging at python.org
Subject: [Neuroimaging] [fmriprep] Pick middle point of ribbon
Dear fmriprep experts,
I found that when fmriprep does projection from EPI to fsaverage space, it equally samples 6 points between pial surface and white-matter surface and averages them. If I want to only pick the middle point of the ribbon, is there a way to modify fmriprep code to achieve this? Thanks!
Regards,
Jingwei
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
From romain.valabregue at upmc.fr Wed Sep 19 09:19:12 2018
From: romain.valabregue at upmc.fr (valabregue)
Date: Wed, 19 Sep 2018 15:19:12 +0200
Subject: [Neuroimaging] non linear deformation
Message-ID:
Dear all
Can anyone point me out some python library to apply non linear
deformation to the image ?
This is for data augmentation so I do not need to do a non linear
registration, but just a way to apply a random smooth deformation field.
Is there in nibabel support for reading deformation field (from spm or
ants) and then to apply it ?
Many thanks
Romain
From fbriend at hotmail.fr Wed Sep 19 09:36:24 2018
From: fbriend at hotmail.fr (=?iso-8859-1?Q?Fr=E9d=E9ric_Briend?=)
Date: Wed, 19 Sep 2018 13:36:24 +0000
Subject: [Neuroimaging] non linear deformation
In-Reply-To:
References:
Message-ID:
Hi Romain,
It seems to me that you could use the elastix registration toolbox of 3D slicer (link). Especially, you will find the python script here.
Best,
Frederic
________________________________
De : Neuroimaging de la part de valabregue
Envoy? : mercredi 19 septembre 2018 15:19:12
? : Neuroimaging analysis in Python
Objet : [Neuroimaging] non linear deformation
Dear all
Can anyone point me out some python library to apply non linear
deformation to the image ?
This is for data augmentation so I do not need to do a non linear
registration, but just a way to apply a random smooth deformation field.
Is there in nibabel support for reading deformation field (from spm or
ants) and then to apply it ?
Many thanks
Romain
_______________________________________________
Neuroimaging mailing list
Neuroimaging at python.org
https://mail.python.org/mailman/listinfo/neuroimaging
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
From matthew.m.mccormick at gmail.com Wed Sep 19 09:39:31 2018
From: matthew.m.mccormick at gmail.com (Matthew McCormick)
Date: Wed, 19 Sep 2018 09:39:31 -0400
Subject: [Neuroimaging] non linear deformation
In-Reply-To:
References:
Message-ID:
Hi Romain,
ITK can help with this task:
python -m pip install --upgrade pip
python -m pip install itk
or
conda -c conda-forge install itk
There are many transforms available, described here:
https://itk.org/ITKSoftwareGuide/html/Book2/ITKSoftwareGuide-Book2ch3.html#x26-1170003.9
HTH,
Matt
On Wed, Sep 19, 2018 at 9:26 AM valabregue
wrote:
> Dear all
>
> Can anyone point me out some python library to apply non linear
> deformation to the image ?
>
> This is for data augmentation so I do not need to do a non linear
> registration, but just a way to apply a random smooth deformation field.
>
> Is there in nibabel support for reading deformation field (from spm or
> ants) and then to apply it ?
>
>
> Many thanks
>
> Romain
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
From alexis.roche at gmail.com Wed Sep 19 09:51:33 2018
From: alexis.roche at gmail.com (Alexis Roche)
Date: Wed, 19 Sep 2018 14:51:33 +0100
Subject: [Neuroimaging] non linear deformation
In-Reply-To:
References:
Message-ID:
Hi Romain,
If it?s just to apply a deformation field, one easy way to go is to use
scipy.ndimage.map_coordinates
Cheers
On Wed 19 Sep 2018 at 14:26, valabregue wrote:
> Dear all
>
> Can anyone point me out some python library to apply non linear
> deformation to the image ?
>
> This is for data augmentation so I do not need to do a non linear
> registration, but just a way to apply a random smooth deformation field.
>
> Is there in nibabel support for reading deformation field (from spm or
> ants) and then to apply it ?
>
>
> Many thanks
>
> Romain
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
--
https://sites.google.com/site/alexisroche
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
From arokem at gmail.com Sat Sep 22 23:18:10 2018
From: arokem at gmail.com (Ariel Rokem)
Date: Sat, 22 Sep 2018 20:18:10 -0700
Subject: [Neuroimaging] non linear deformation
In-Reply-To:
References:
Message-ID:
Hi Romain,
Dipy has a full implementation of the symmetric diffeomorphic registration:
http://nipy.org/dipy/examples_built/syn_registration_3d.html
If you already have your deformation field, you can use that to initialize
a dipy.align.imwarp.DiffeomorphicMap object and apply the transformation to
your input image.
Hope that helps,
Ariel
On Wed, Sep 19, 2018 at 6:51 AM Alexis Roche wrote:
> Hi Romain,
>
> If it?s just to apply a deformation field, one easy way to go is to use
> scipy.ndimage.map_coordinates
>
> Cheers
>
> On Wed 19 Sep 2018 at 14:26, valabregue wrote:
>
>> Dear all
>>
>> Can anyone point me out some python library to apply non linear
>> deformation to the image ?
>>
>> This is for data augmentation so I do not need to do a non linear
>> registration, but just a way to apply a random smooth deformation field.
>>
>> Is there in nibabel support for reading deformation field (from spm or
>> ants) and then to apply it ?
>>
>>
>> Many thanks
>>
>> Romain
>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
> --
> https://sites.google.com/site/alexisroche
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: