From missjy at connect.hku.hk  Mon Mar  2 07:17:05 2020
From: missjy at connect.hku.hk (JIAYING CHEN)
Date: Mon, 2 Mar 2020 20:17:05 +0800
Subject: [Neuroimaging] Query on fmriprep
Message-ID: <F6670C01-3530-489A-BE13-1D1281E7A125@connect.hku.hk>

Hi,

I?m dealing with frmiprep these days, and I met a problem not knowing how to deal with it. I followed the tutorials online to run fmriprep, but it seemed that it can only deal with files in BIDS format. In order to transform the files into BIDS format, I need to use .dcm files. However, I only have .nii files at hand, which seems like a half-processed one.

Could you please tell me what to do regarding this issue? Your reply will be much appreciated.

Best regards,
Jiaying

From christophe at pallier.org  Mon Mar  2 08:19:38 2020
From: christophe at pallier.org (Christophe Pallier)
Date: Mon, 2 Mar 2020 14:19:38 +0100
Subject: [Neuroimaging] Query on fmriprep
In-Reply-To: <F6670C01-3530-489A-BE13-1D1281E7A125@connect.hku.hk>
References: <F6670C01-3530-489A-BE13-1D1281E7A125@connect.hku.hk>
Message-ID: <CALyk9bxRC8dDESp2BTKrr-DeriyRWt05+riBY6+nu2NZsED8Tw@mail.gmail.com>

BIDS is not a file format but a convention to name and organize files (see
https://bids.neuroimaging.io/).
In BIDS, image files actually use the nifti (.nii) format.

--
Christophe Pallier (http://www.pallier.org)
INSERM Cognitive Neuroimaging Lab (http://www.unicog.org)


On Mon, Mar 2, 2020 at 1:31 PM JIAYING CHEN <missjy at connect.hku.hk> wrote:

> Hi,
>
> I?m dealing with frmiprep these days, and I met a problem not knowing how
> to deal with it. I followed the tutorials online to run fmriprep, but it
> seemed that it can only deal with files in BIDS format. In order to
> transform the files into BIDS format, I need to use .dcm files. However, I
> only have .nii files at hand, which seems like a half-processed one.
>
> Could you please tell me what to do regarding this issue? Your reply will
> be much appreciated.
>
> Best regards,
> Jiaying
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From frakkopesto at gmail.com  Mon Mar  2 10:10:40 2020
From: frakkopesto at gmail.com (Franco Pestilli)
Date: Mon, 2 Mar 2020 10:10:40 -0500
Subject: [Neuroimaging] Query on fmriprep
In-Reply-To: <F6670C01-3530-489A-BE13-1D1281E7A125@connect.hku.hk>
References: <F6670C01-3530-489A-BE13-1D1281E7A125@connect.hku.hk>
Message-ID: <2199C92A-84F8-4A07-B036-4901AB3E7777@gmail.com>

Hi Jiaying.

Have you looked at the web service implementing FMRIPREP on brainlife.io?
https://doi.org/10.25663/brainlife.app.160
https://doi.org/10.25663/brainlife.app.267

The platform is free to use and would allow uploading nifty files and process them with FMRIPREP. After data processing, you could download the results in BIDS format. Here is some information to get your started:
https://brainlife.io/docs/ <https://brainlife.io/docs/>
https://brainlife.io/docs/tutorial/fmri-preprocessing-tutorial/ <https://brainlife.io/docs/tutorial/fmri-preprocessing-tutorial/>

I hope this helps.

Best regards,
Franco

Franco Pestilli, PhD
Associate Professor
Psychology <http://psych.indiana.edu/>, Neuroscience <http://www.indiana.edu/~neurosci/> and Cognitive Science <http://www.cogs.indiana.edu/> 
Engineering <https://www.engineering.indiana.edu/people/profile.html?profile_id=528>, Computer Science <https://www.cs.indiana.edu/>, and Optometry <http://optometry.iu.edu/> by courtesy
? Indiana University <http://www.iub.edu/>
Principal Midwest Big Data Hub <http://midwestbigdatahub.org/>
Microsoft Faculty Fellow <https://www.microsoft.com/en-us/research/blog/microsoft-investigator-fellows-accelerate-scientific-and-teaching-impact-with-azure-cloud-computing/?fbclid=IwAR2adMlfl3uhr8gCdp36ivFqgdD5-9Bwp8imnxredAdQ0O3Ae8JM6ntBgDg> | brainlife.io <http://www.brain-life.org/> 

> On Mar 2, 2020, at 7:17 AM, JIAYING CHEN <missjy at connect.hku.hk> wrote:
> 
> Hi,
> 
> I?m dealing with frmiprep these days, and I met a problem not knowing how to deal with it. I followed the tutorials online to run fmriprep, but it seemed that it can only deal with files in BIDS format. In order to transform the files into BIDS format, I need to use .dcm files. However, I only have .nii files at hand, which seems like a half-processed one.
> 
> Could you please tell me what to do regarding this issue? Your reply will be much appreciated.
> 
> Best regards,
> Jiaying
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging

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From baptiste.plantin at altran.com  Mon Mar  2 10:57:38 2020
From: baptiste.plantin at altran.com (PLANTIN Baptiste)
Date: Mon, 2 Mar 2020 15:57:38 +0000
Subject: [Neuroimaging] 2 questions about Image processing on nifti
 images
Message-ID: <42E126B2488FED44A5647DC18C0D5D10DB4B92FB@XMB-DCFR-35.europe.corp.altran.com>

Hi again !

OK I get a bit more why I can't do that so easily : I extracted the slices of the NIFTI image ("img_sobel_data"), filtered them, but I wasn't change the NIFTI image itself !!!

    img = nib.load(im_path)
    img_sobel = nib.load(im_path)

    # Name the interested data
    img_data = img.get_fdata()
    img_sobel_data = img_sobel.get_fdata()

    header = img.header
    nb_img = header.get_data_shape()
    nb_img_h = nb_img[2] #Hauteur

    for sl in range(0,nb_img_h):
            slice_h = img_data[:, :, sl]
            #Sobel
            sx = ndimage.sobel(slice_h, axis=0, mode='constant')
            sy = ndimage.sobel(slice_h, axis=1, mode='constant')
            sobel_h = np.hypot(sx, sy)

            img_sobel_data[:, :, sl] = sobel_h #Change the image slice to the sobel one
# Save Sobel:
nib.save(img_sobel,imSobel_path)

So my question now : How to change the NIFTI image get from img_sobel.get_fdata() ?

Have a nice week !


De : PLANTIN Baptiste
Envoy? : vendredi 28 f?vrier 2020 15:22
? : 'neuroimaging at python.org' <neuroimaging at python.org>
Objet : 2 questions about Image processing on nifti images

Hello team,

Looking recently about MRI, I'm starting to work using your tool and I have two questions, one relative to a method and one about dataset nii.gz :

-        I'm actually use the Sobel filter on a .nii slices. If the process is successfully done, I don't know how to create a new nifty image as a Sobel version of the original one. I tried this method:

?        Load the original nifty image as "img"

?        Load again the original image as "Sobel"

?        Use the Sobel filtering on each slices

?        For each slices (for loop), replace the slice in "Sobel" to the new filtered slice

?        Save the new Sobel image in the file as "imSobelNumX"

This method don't work, it seems the slices are not replaced. It is due to the particular format or it is due to Python compiler ?


-        Is there are a nii.gz dataset of the entire (And healthy) body somewhere in order to use it as reference for detection ? I found only a GIF in internet actually (http://www.madsci.org/~lynn/VH/Transverse.gif)

Thank you and best regards,

Cordialement,
Baptiste PLANTIN

Ing?nieur Consultant
ALTRAN IDF
baptiste.plantin at altran.com<mailto:baptiste.plantin at altran.com>

[cid:image003.jpg at 01D2E8E2.CBD89F30]
2, rue Paul Dautier
78457 V?lizy Villacoublay
FRANCE
www.altran.com/fr<http://www.altran.com/fr%0d>
[cid:image004.jpg at 01D2E8E2.CBD89F30]<https://twitter.com/AltranFR>  [cid:image005.jpg at 01D2E8E2.CBD89F30] <https://www.facebook.com/AltranFrance>    [cid:image006.jpg at 01D2E8E2.CBD89F30] <https://www.linkedin.com/company-beta/3124/>

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From matthew.brett at gmail.com  Wed Mar  4 09:34:46 2020
From: matthew.brett at gmail.com (Matthew Brett)
Date: Wed, 4 Mar 2020 14:34:46 +0000
Subject: [Neuroimaging] 2 questions about Image processing on nifti
 images
In-Reply-To: <42E126B2488FED44A5647DC18C0D5D10DB4B92FB@XMB-DCFR-35.europe.corp.altran.com>
References: <42E126B2488FED44A5647DC18C0D5D10DB4B92FB@XMB-DCFR-35.europe.corp.altran.com>
Message-ID: <CAH6Pt5penY1JcPh+pJfGCQgMgX2p-VJV2TbhA08Vh++XOsPa-w@mail.gmail.com>

Hi,

On Wed, Mar 4, 2020 at 2:30 PM PLANTIN Baptiste
<baptiste.plantin at altran.com> wrote:
>
> Hi again !
>
>
>
> OK I get a bit more why I can't do that so easily : I extracted the slices of the NIFTI image (?img_sobel_data?), filtered them, but I wasn't change the NIFTI image itself !!!
>
>
>
>     img = nib.load(im_path)
>
>     img_sobel = nib.load(im_path)
>
>
>
>     # Name the interested data
>
>     img_data = img.get_fdata()
>
>     img_sobel_data = img_sobel.get_fdata()
>
>
>
>     header = img.header
>
>     nb_img = header.get_data_shape()
>
>     nb_img_h = nb_img[2] #Hauteur
>
>
>
>     for sl in range(0,nb_img_h):
>
>             slice_h = img_data[:, :, sl]
>
>             #Sobel
>
>             sx = ndimage.sobel(slice_h, axis=0, mode='constant')
>
>             sy = ndimage.sobel(slice_h, axis=1, mode='constant')
>
>             sobel_h = np.hypot(sx, sy)
>
>
>
>             img_sobel_data[:, :, sl] = sobel_h #Change the image slice to the sobel one
>
> # Save Sobel:
>
> nib.save(img_sobel,imSobel_path)
>
>
>
> So my question now : How to change the NIFTI image get from img_sobel.get_fdata() ?

Have a look at my example in the earlier email.  The trick is to make
a new array, fill it with the data you want, and then make a new image
with that array:

filtered_image = nib.Nifti1Image(new_array, None, nb_img.header)
nib.save(filtered_image, 'my_file_name.nii')

Cheers,

Matthew

From markiewicz at stanford.edu  Mon Mar  9 10:26:14 2020
From: markiewicz at stanford.edu (Christopher Markiewicz)
Date: Mon, 9 Mar 2020 14:26:14 +0000
Subject: [Neuroimaging] ANN: NiBabel 3.0.2
Message-ID: <MN2PR02MB6752330E5A40680CBA5FC1D3A9FE0@MN2PR02MB6752.namprd02.prod.outlook.com>

Hi all,

Just a quick note that NiBabel 3.0.2 is out. NiBabel 3.0.1 (which I failed to announce) and 3.0.2 are very minor bug fix releases that should mostly affect developers and package maintainers, and users should see no particular benefit to upgrading. Users that have h5py installed but are not using MINC2 should see a slightly reduced import time, thanks to Yarik.

The next planned release is a feature release (3.1.0), with an estimated release time in a month or so.

NiBabel can be cited via its Zenodo archives: https://doi.org/10.5281/zenodo.3701467

Full changelog follows.

----

Most work on NiBabel so far has been by Matthew Brett (MB), Chris Markiewicz
(CM), Michael Hanke (MH), Marc-Alexandre C?t? (MC), Ben Cipollini (BC), Paul
McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh (SG),
Eric Larson (EL), Demian Wassermann, and Stephan Gerhard.

References like "pr/298" refer to github pull request numbers.

3.0.2 (Monday 9 March 2020)
===========================

Bug fixes
---------
* Attempt to find versioneer version when building docs (pr/894) (CM)
* Delay import of h5py until neded (backport of pr/889) (YOH, reviewed by CM)

Maintenance
-----------
* Fix typo in documentation (backport of pr/893) (Zvi Baratz, reviewed by CM)
* Set minimum matplotlib to 1.5.3 to ensure wheels are available on all
  supported Python versions. (backport of pr/887) (CM)
* Remove ``pyproject.toml`` for now. (issue/859) (CM)


--

Chris Markiewicz

Center for Reproducible Neuroscience

Stanford University
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From satra at mit.edu  Mon Mar  9 10:31:28 2020
From: satra at mit.edu (Satrajit Ghosh)
Date: Mon, 9 Mar 2020 10:31:28 -0400
Subject: [Neuroimaging] ANN: NiBabel 3.0.2
In-Reply-To: <MN2PR02MB6752330E5A40680CBA5FC1D3A9FE0@MN2PR02MB6752.namprd02.prod.outlook.com>
References: <MN2PR02MB6752330E5A40680CBA5FC1D3A9FE0@MN2PR02MB6752.namprd02.prod.outlook.com>
Message-ID: <CA+A4wOnp03DiFJ5xKL4yc9PmnQkL9yBCKUKt_eB8oq8R=bEJkw@mail.gmail.com>

thanks chris!

i'll also use this opportunity to ask the community that if you or people
in your research groups can help chris maintain nibabel, please consider
supporting him. this should not take a lot of time, and will spread some of
the knowledge of maintenance as well.

cheers,

satra

On Mon, Mar 9, 2020 at 10:28 AM Christopher Markiewicz <
markiewicz at stanford.edu> wrote:

> Hi all,
>
> Just a quick note that NiBabel 3.0.2 is out. NiBabel 3.0.1 (which I failed
> to announce) and 3.0.2 are very minor bug fix releases that should mostly
> affect developers and package maintainers, and users should see no
> particular benefit to upgrading. Users that have h5py installed but are not
> using MINC2 should see a slightly reduced import time, thanks to Yarik.
>
> The next planned release is a feature release (3.1.0), with an estimated
> release time in a month or so.
>
> NiBabel can be cited via its Zenodo archives:
> https://doi.org/10.5281/zenodo.3701467
>
> Full changelog follows.
>
> ----
>
> Most work on NiBabel so far has been by Matthew Brett (MB), Chris
> Markiewicz
> (CM), Michael Hanke (MH), Marc-Alexandre C?t? (MC), Ben Cipollini (BC),
> Paul
> McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh
> (SG),
> Eric Larson (EL), Demian Wassermann, and Stephan Gerhard.
>
> References like "pr/298" refer to github pull request numbers.
>
> 3.0.2 (Monday 9 March 2020)
> ===========================
>
> Bug fixes
> ---------
> * Attempt to find versioneer version when building docs (pr/894) (CM)
> * Delay import of h5py until neded (backport of pr/889) (YOH, reviewed by
> CM)
>
> Maintenance
> -----------
> * Fix typo in documentation (backport of pr/893) (Zvi Baratz, reviewed by
> CM)
> * Set minimum matplotlib to 1.5.3 to ensure wheels are available on all
>   supported Python versions. (backport of pr/887) (CM)
> * Remove ``pyproject.toml`` for now. (issue/859) (CM)
>
> --
>
> Chris Markiewicz
>
> Center for Reproducible Neuroscience
>
> Stanford University
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From matthew.brett at gmail.com  Mon Mar  9 10:35:08 2020
From: matthew.brett at gmail.com (Matthew Brett)
Date: Mon, 9 Mar 2020 14:35:08 +0000
Subject: [Neuroimaging] ANN: NiBabel 3.0.2
In-Reply-To: <MN2PR02MB6752330E5A40680CBA5FC1D3A9FE0@MN2PR02MB6752.namprd02.prod.outlook.com>
References: <MN2PR02MB6752330E5A40680CBA5FC1D3A9FE0@MN2PR02MB6752.namprd02.prod.outlook.com>
Message-ID: <CAH6Pt5oz7k=exnTmOrK_OSaV6BLAmkv-u7gm7bHKq=qJHaJjgQ@mail.gmail.com>

Hi Chris,

Thanks much, as ever.

Cheers,

Matthew

On Mon, Mar 9, 2020 at 2:28 PM Christopher Markiewicz
<markiewicz at stanford.edu> wrote:
>
> Hi all,
>
> Just a quick note that NiBabel 3.0.2 is out. NiBabel 3.0.1 (which I failed to announce) and 3.0.2 are very minor bug fix releases that should mostly affect developers and package maintainers, and users should see no particular benefit to upgrading. Users that have h5py installed but are not using MINC2 should see a slightly reduced import time, thanks to Yarik.
>
> The next planned release is a feature release (3.1.0), with an estimated release time in a month or so.
>
> NiBabel can be cited via its Zenodo archives: https://doi.org/10.5281/zenodo.3701467
>
> Full changelog follows.
>
> ----
>
> Most work on NiBabel so far has been by Matthew Brett (MB), Chris Markiewicz
> (CM), Michael Hanke (MH), Marc-Alexandre C?t? (MC), Ben Cipollini (BC), Paul
> McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh (SG),
> Eric Larson (EL), Demian Wassermann, and Stephan Gerhard.
>
> References like "pr/298" refer to github pull request numbers.
>
> 3.0.2 (Monday 9 March 2020)
> ===========================
>
> Bug fixes
> ---------
> * Attempt to find versioneer version when building docs (pr/894) (CM)
> * Delay import of h5py until neded (backport of pr/889) (YOH, reviewed by CM)
>
> Maintenance
> -----------
> * Fix typo in documentation (backport of pr/893) (Zvi Baratz, reviewed by CM)
> * Set minimum matplotlib to 1.5.3 to ensure wheels are available on all
>   supported Python versions. (backport of pr/887) (CM)
> * Remove ``pyproject.toml`` for now. (issue/859) (CM)
>
> --
>
> Chris Markiewicz
>
> Center for Reproducible Neuroscience
>
> Stanford University
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging

From bertrand.thirion at inria.fr  Mon Mar  9 10:47:48 2020
From: bertrand.thirion at inria.fr (bthirion)
Date: Mon, 9 Mar 2020 15:47:48 +0100
Subject: [Neuroimaging] ANN: NiBabel 3.0.2
In-Reply-To: <MN2PR02MB6752330E5A40680CBA5FC1D3A9FE0@MN2PR02MB6752.namprd02.prod.outlook.com>
References: <MN2PR02MB6752330E5A40680CBA5FC1D3A9FE0@MN2PR02MB6752.namprd02.prod.outlook.com>
Message-ID: <e37821d4-830b-bf45-3d90-7bd124711a8f@inria.fr>

Congratulations and thx for the wonderful work !
B

On 09/03/2020 15:26, Christopher Markiewicz wrote:
> Hi all,
>
> Just a quick note that NiBabel 3.0.2 is out. NiBabel 3.0.1 (which I 
> failed to announce) and 3.0.2 are very minor bug fix releases that 
> should mostly affect developers and package maintainers, and users 
> should see no particular benefit to upgrading. Users that have h5py 
> installed but are not using MINC2 should see a slightly reduced import 
> time, thanks to Yarik.
>
> The next planned release is a feature release (3.1.0), with an 
> estimated release time in a month or so.
>
> NiBabel can be cited via its Zenodo archives: 
> https://doi.org/10.5281/zenodo.3701467 
> <https://doi.org/10.5281/zenodo.3701467>
>
> Full changelog follows.
>
> ----
>
> Most work on NiBabel so far has been by Matthew Brett (MB), Chris 
> Markiewicz
> (CM), Michael Hanke (MH), Marc-Alexandre C?t? (MC), Ben Cipollini 
> (BC), Paul
> McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh 
> (SG),
> Eric Larson (EL), Demian Wassermann, and Stephan Gerhard.
>
> References like "pr/298" refer to github pull request numbers.
>
> 3.0.2 (Monday 9 March 2020)
> ===========================
>
> Bug fixes
> ---------
> * Attempt to find versioneer version when building docs (pr/894) (CM)
> * Delay import of h5py until neded (backport of pr/889) (YOH, reviewed 
> by CM)
>
> Maintenance
> -----------
> * Fix typo in documentation (backport of pr/893) (Zvi Baratz, reviewed 
> by CM)
> * Set minimum matplotlib to 1.5.3 to ensure wheels are available on all
> ? supported Python versions. (backport of pr/887) (CM)
> * Remove ``pyproject.toml`` for now. (issue/859) (CM)
>
> -- 
>
> Chris Markiewicz
>
> Center for Reproducible Neuroscience
>
> Stanford University
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging


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From gael.varoquaux at normalesup.org  Mon Mar  9 16:28:59 2020
From: gael.varoquaux at normalesup.org (Gael Varoquaux)
Date: Mon, 9 Mar 2020 16:28:59 -0400
Subject: [Neuroimaging] ANN: NiBabel 3.0.2
In-Reply-To: <MN2PR02MB6752330E5A40680CBA5FC1D3A9FE0@MN2PR02MB6752.namprd02.prod.outlook.com>
References: <MN2PR02MB6752330E5A40680CBA5FC1D3A9FE0@MN2PR02MB6752.namprd02.prod.outlook.com>
Message-ID: <20200309202859.jpe5vxx7gwdb3iax@phare.normalesup.org>

Thank you Chris and all the nibabel team.

Indeed, we should all cite Nibabel (note to self). It's important!

Ga?l

On Mon, Mar 09, 2020 at 02:26:14PM +0000, Christopher Markiewicz wrote:
> Hi all,

> Just a quick note that NiBabel 3.0.2 is out. NiBabel 3.0.1 (which I failed to
> announce) and 3.0.2 are very minor bug fix releases that should mostly affect
> developers and package maintainers, and users should see no particular benefit
> to upgrading. Users that have h5py installed but are not using MINC2 should see
> a slightly reduced import time, thanks to Yarik.

> The next planned release is a feature release (3.1.0), with an estimated
> release time in a month or so.

> NiBabel can be cited via its Zenodo archives: https://doi.org/10.5281/
> zenodo.3701467

> Full changelog follows.

> ----

> Most work on NiBabel so far has been by Matthew Brett (MB), Chris Markiewicz
> (CM), Michael Hanke (MH), Marc-Alexandre C?t? (MC), Ben Cipollini (BC), Paul
> McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh (SG),
> Eric Larson (EL), Demian Wassermann, and Stephan Gerhard.

> References like "pr/298" refer to github pull request numbers.

> 3.0.2 (Monday 9 March 2020)
> ===========================

> Bug fixes
> ---------
> * Attempt to find versioneer version when building docs (pr/894) (CM)
> * Delay import of h5py until neded (backport of pr/889) (YOH, reviewed by CM)

> Maintenance
> -----------
> * Fix typo in documentation (backport of pr/893) (Zvi Baratz, reviewed by CM)
> * Set minimum matplotlib to 1.5.3 to ensure wheels are available on all
>   supported Python versions. (backport of pr/887) (CM)
> * Remove ``pyproject.toml`` for now. (issue/859) (CM)
-- 
    Gael Varoquaux
    Research Director, INRIA		  Visiting professor, McGill 
    http://gael-varoquaux.info            http://twitter.com/GaelVaroquaux

From jbpoline at gmail.com  Mon Mar  9 16:31:49 2020
From: jbpoline at gmail.com (JB Poline)
Date: Mon, 9 Mar 2020 16:31:49 -0400
Subject: [Neuroimaging] ANN: NiBabel 3.0.2
In-Reply-To: <20200309202859.jpe5vxx7gwdb3iax@phare.normalesup.org>
References: <MN2PR02MB6752330E5A40680CBA5FC1D3A9FE0@MN2PR02MB6752.namprd02.prod.outlook.com>
 <20200309202859.jpe5vxx7gwdb3iax@phare.normalesup.org>
Message-ID: <CALMaa81-ZH62C3yfEAZbdXgwVYGFbADVqC5uYdg+5G8dPZSHnA@mail.gmail.com>

Many thanks Indeed - and note to myself as well !
JB

On Mon, Mar 9, 2020 at 4:29 PM Gael Varoquaux <gael.varoquaux at normalesup.org>
wrote:

> Thank you Chris and all the nibabel team.
>
> Indeed, we should all cite Nibabel (note to self). It's important!
>
> Ga?l
>
> On Mon, Mar 09, 2020 at 02:26:14PM +0000, Christopher Markiewicz wrote:
> > Hi all,
>
> > Just a quick note that NiBabel 3.0.2 is out. NiBabel 3.0.1 (which I
> failed to
> > announce) and 3.0.2 are very minor bug fix releases that should mostly
> affect
> > developers and package maintainers, and users should see no particular
> benefit
> > to upgrading. Users that have h5py installed but are not using MINC2
> should see
> > a slightly reduced import time, thanks to Yarik.
>
> > The next planned release is a feature release (3.1.0), with an estimated
> > release time in a month or so.
>
> > NiBabel can be cited via its Zenodo archives: https://doi.org/10.5281/
> > zenodo.3701467
>
> > Full changelog follows.
>
> > ----
>
> > Most work on NiBabel so far has been by Matthew Brett (MB), Chris
> Markiewicz
> > (CM), Michael Hanke (MH), Marc-Alexandre C?t? (MC), Ben Cipollini (BC),
> Paul
> > McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh
> (SG),
> > Eric Larson (EL), Demian Wassermann, and Stephan Gerhard.
>
> > References like "pr/298" refer to github pull request numbers.
>
> > 3.0.2 (Monday 9 March 2020)
> > ===========================
>
> > Bug fixes
> > ---------
> > * Attempt to find versioneer version when building docs (pr/894) (CM)
> > * Delay import of h5py until neded (backport of pr/889) (YOH, reviewed
> by CM)
>
> > Maintenance
> > -----------
> > * Fix typo in documentation (backport of pr/893) (Zvi Baratz, reviewed
> by CM)
> > * Set minimum matplotlib to 1.5.3 to ensure wheels are available on all
> >   supported Python versions. (backport of pr/887) (CM)
> > * Remove ``pyproject.toml`` for now. (issue/859) (CM)
> --
>     Gael Varoquaux
>     Research Director, INRIA              Visiting professor, McGill
>     http://gael-varoquaux.info            http://twitter.com/GaelVaroquaux
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From code at oscaresteban.es  Mon Mar 23 13:15:48 2020
From: code at oscaresteban.es (Oscar Esteban)
Date: Mon, 23 Mar 2020 10:15:48 -0700
Subject: [Neuroimaging] Query on fmriprep
In-Reply-To: <F6670C01-3530-489A-BE13-1D1281E7A125@connect.hku.hk>
References: <F6670C01-3530-489A-BE13-1D1281E7A125@connect.hku.hk>
Message-ID: <CAAsFcgxHPJUiTmYmrdYCi7TobM9CipntDvOCyY0QKsTpyB3uMA@mail.gmail.com>

Hi Jiaying,

fMRIPrep only works on acquired data - i.e., if your files are somewhat
preprocessed other than defacing of anatomical images it won't work.

I think the BIDS Starter Kit
<https://github.com/bids-standard/bids-starter-kit> could help you navigate
through the conversion process. That said, you are right it will not be
straightforward if your data are already in NIfTI format - hopefully none
of the crucial metadata have been lost in the process.

For questions about BIDS or fMRIPrep, I would recommend
https://neurostars.org.

Cheers,
Oscar


On Mon, Mar 2, 2020 at 4:31 AM JIAYING CHEN <missjy at connect.hku.hk> wrote:

> Hi,
>
> I?m dealing with frmiprep these days, and I met a problem not knowing how
> to deal with it. I followed the tutorials online to run fmriprep, but it
> seemed that it can only deal with files in BIDS format. In order to
> transform the files into BIDS format, I need to use .dcm files. However, I
> only have .nii files at hand, which seems like a half-processed one.
>
> Could you please tell me what to do regarding this issue? Your reply will
> be much appreciated.
>
> Best regards,
> Jiaying
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From aaron.b.tanenbaum at gmail.com  Wed Mar 25 01:19:48 2020
From: aaron.b.tanenbaum at gmail.com (Aaron Tanenbaum)
Date: Wed, 25 Mar 2020 00:19:48 -0500
Subject: [Neuroimaging] Spacetimerealign
Message-ID: <CAAGp_pySgfR8pK1f787Zh91O5765=aCn4u_NUyBh-rDOK3C-iQ@mail.gmail.com>

I have two questions.
First, how do you get the 6 motion parameters from the function
SpacetimeRealign. I suspect this may not be possible.

Second. I have a several transforms to get our fMRI data from native to
common space. I am trying to figure out how to combine these transforms
along with the transform generated by  SpacetimeRealign to achieve a one
step resample. Is there a way to doing this
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From alexandre.gramfort at inria.fr  Sat Mar 28 04:47:20 2020
From: alexandre.gramfort at inria.fr (Alexandre Gramfort)
Date: Sat, 28 Mar 2020 09:47:20 +0100
Subject: [Neuroimaging] [ANN] MNE-Python 0.20
Message-ID: <CADeotZpczGNBrpDNPAFUoj_k3nUcg4YR4ARWvcOFKQ5GzcDEeQ@mail.gmail.com>

Hi,

First we hope that you?re safe in these troubled times.

We are pleased to announce the new 0.20 release of MNE-Python (
https://mne.tools/ <https://mne.tools/stable/index.html>)

A few highlights

============

   -

   PyVista 0.24 is now available for 3D plotting (alternative to mayavi).
   This is a big step forward for source space data visualization that allows
   users to explore time interactively, pick vertices to view their time
   activation courses, (auto-)adjust color scales, etc. To use it, `pip
   install -U pyvista` and then in your Python script do
   `mne.viz.set_3d_backend(?pyvista?)`. You should then be good to go: Simply
   plot your source-time course data via stc.plot(), and the improved
   interface should open automatically!
   -

   Automatic estimation of head motion from cHPI MEG coils in the mne.chpi
   namespace.
   -

   Automatic detection of bad (flat or overly noisy) MEG channels via the
   new find_bad_channels_maxwell function
   -

   New topography plotting code to take into account head position and deal
   properly with channel subsets
   -

   New function and tutorial for estimating source-power from covariance
   matrices using MNE (as commonly done with a beamformer).
   -

   Extensive improvements to the narrative documentation
   https://mne.tools/stable/auto_tutorials/index.html


Notable API changes

================

   -

   Sensors shown in relationship to a head circle, as in topomap plotting,
   are now systematically converted from their given physical locations. Using
   a static layout (such as those typically used with topo plots) has been
   deprecated.


For a full list of improvements and API changes, see:

https://mne.tools/stable/whats_new.html#version-0-20

To install the latest release the following command should do the job:

pip install --upgrade --user mne

As usual we welcome your bug reports, feature requests, critiques, and

contributions.

Some links:

- https://github.com/mne-tools/mne-python (code + readme on how to install)

- <http://martinos.org/mne/stable/>https://mne.tools/
<https://mne.tools/stable/index.html> (full MNE documentation)

Follow us on Twitter: https://twitter.com/mne_news

Stay safe and take care !

Regards,

The MNE-Python developers

People who contributed to this release (in alphabetical order):


   -

   Adam Li
   -

   Adonay Nunes
   -

   Alex Rockhill
   -

   Alexandre Gramfort
   -

   Ariel Rokem
   -

   Britta Westner
   -

   Carlos de la Torre
   -

   Christian Brodbeck
   -

   Christian O?Reilly
   -

   Chun-Hui Li
   -

   Clemens Brunner
   -

   Daniel McCloy
   -

   Demetres Kostas
   -

   Denis A. Engemann
   -

   Dmitrii Altukhov
   -

   Dominik Welke
   -

   Eric Larson
   -

   Ezequiel Mikulan
   -

   Fahimeh Mamashli
   -

   Fede Raimondo
   -

   Fu-Te Wong
   -

   Geoff Brookshire
   -

   Guillaume Favelier
   -

   Henrich Kolkhorst
   -

   Joan Massich
   -

   Jos? C. Garc?a Alanis
   -

   Jussi Nurminen
   -

   Kaisu Lankinen
   -

   Luke Bloy
   -

   Mainak Jas
   -

   Marijn van Vliet
   -

   Mathurin Massias
   -

   Mikolaj Magnuski
   -

   Mohamed Sherif
   -

   Mohammad Daneshzand
   -

   Nataliia Kozhemiako
   -

   Nicolas Barascud
   -

   Nicolas Legrand
   -

   Olaf Hauk
   -

   Padma Sundaram
   -

   Ramiro Gatti
   -

   Richard H?chenberger
   -

   Robert Luke
   -

   Robert Oostenveld
   -

   Sebastian Major
   -

   Sophie Herbst
   -

   Stefan Appelhoff
   -

   Stefan Repplinger
   -

   Thomas Hartmann
   -

   Victor F?rat
   -

   Yu-Han Luo
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From bertrand.thirion at inria.fr  Sat Mar 28 04:59:22 2020
From: bertrand.thirion at inria.fr (bthirion)
Date: Sat, 28 Mar 2020 09:59:22 +0100
Subject: [Neuroimaging] [ANN] MNE-Python 0.20
In-Reply-To: <CADeotZpczGNBrpDNPAFUoj_k3nUcg4YR4ARWvcOFKQ5GzcDEeQ@mail.gmail.com>
References: <CADeotZpczGNBrpDNPAFUoj_k3nUcg4YR4ARWvcOFKQ5GzcDEeQ@mail.gmail.com>
Message-ID: <c9ee7953-a05c-bc7d-4fd0-c8304d897ef9@inria.fr>

Congratulations for all the plotting improvements.
B

On 28/03/2020 09:47, Alexandre Gramfort wrote:
>
> Hi,
>
>
> First we hope that you?re safe in these troubled times.
>
>
> We are pleased to announce the new 0.20 release of MNE-Python 
> (https://mne.tools/ <https://mne.tools/stable/index.html>)
>
>
> A few highlights
>
> ============
>
>  *
>
>     PyVista 0.24 is now available for 3D plotting (alternative to
>     mayavi). This is a big step forward for source space data
>     visualization that allows users to explore time interactively,
>     pick vertices to view their time activation courses, (auto-)adjust
>     color scales, etc. To use it, `pip install -U pyvista` and then in
>     your Python script do `mne.viz.set_3d_backend(?pyvista?)`. You
>     should then be good to go: Simply plot your source-time course
>     data via stc.plot(), and the improved interface should open
>     automatically!
>
>  *
>
>     Automatic estimation of head motion from cHPI MEG coils in the
>     mne.chpi namespace.
>
>  *
>
>     Automatic detection of bad (flat or overly noisy) MEG channels via
>     the new find_bad_channels_maxwell function
>
>  *
>
>     New topography plotting code to take into account head position
>     and deal properly with channel subsets
>
>  *
>
>     New function and tutorial for estimating source-power from
>     covariance matrices using MNE (as commonly done with a beamformer).
>
>  *
>
>     Extensive improvements to the narrative documentation
>     https://mne.tools/stable/auto_tutorials/index.html
>
>
> Notable API changes
>
> ================
>
>  *
>
>     Sensors shown in relationship to a head circle, as in topomap
>     plotting, are now systematically converted from their given
>     physical locations. Using a static layout (such as those typically
>     used with topo plots) has been deprecated.
>
>
> For a full list of improvements and API changes, see:
>
>
> https://mne.tools/stable/whats_new.html#version-0-20
>
>
> To install the latest release the following command should do the job:
>
>
> pip install --upgrade --user mne
>
>
> As usual we welcome your bug reports, feature requests, critiques, and
>
> contributions.
>
>
> Some links:
>
>
> -https://github.com/mne-tools/mne-python 
> <https://github.com/mne-tools/mne-python>(code + readme on how to install)
>
> -<http://martinos.org/mne/stable/>https://mne.tools/ 
> <https://mne.tools/stable/index.html>(full MNE documentation)
>
>
> Follow us on Twitter:https://twitter.com/mne_news 
> <https://twitter.com/mne_news>
>
>
> Stay safe and take care !
>
>
> Regards,
>
> The MNE-Python developers
>
>
> People who contributed to this release (in alphabetical order):
>
>
>  *
>
>     Adam Li
>
>  *
>
>     Adonay Nunes
>
>  *
>
>     Alex Rockhill
>
>  *
>
>     Alexandre Gramfort
>
>  *
>
>     Ariel Rokem
>
>  *
>
>     Britta Westner
>
>  *
>
>     Carlos de la Torre
>
>  *
>
>     Christian Brodbeck
>
>  *
>
>     Christian O?Reilly
>
>  *
>
>     Chun-Hui Li
>
>  *
>
>     Clemens Brunner
>
>  *
>
>     Daniel McCloy
>
>  *
>
>     Demetres Kostas
>
>  *
>
>     Denis A. Engemann
>
>  *
>
>     Dmitrii Altukhov
>
>  *
>
>     Dominik Welke
>
>  *
>
>     Eric Larson
>
>  *
>
>     Ezequiel Mikulan
>
>  *
>
>     Fahimeh Mamashli
>
>  *
>
>     Fede Raimondo
>
>  *
>
>     Fu-Te Wong
>
>  *
>
>     Geoff Brookshire
>
>  *
>
>     Guillaume Favelier
>
>  *
>
>     Henrich Kolkhorst
>
>  *
>
>     Joan Massich
>
>  *
>
>     Jos? C. Garc?a Alanis
>
>  *
>
>     Jussi Nurminen
>
>  *
>
>     Kaisu Lankinen
>
>  *
>
>     Luke Bloy
>
>  *
>
>     Mainak Jas
>
>  *
>
>     Marijn van Vliet
>
>  *
>
>     Mathurin Massias
>
>  *
>
>     Mikolaj Magnuski
>
>  *
>
>     Mohamed Sherif
>
>  *
>
>     Mohammad Daneshzand
>
>  *
>
>     Nataliia Kozhemiako
>
>  *
>
>     Nicolas Barascud
>
>  *
>
>     Nicolas Legrand
>
>  *
>
>     Olaf Hauk
>
>  *
>
>     Padma Sundaram
>
>  *
>
>     Ramiro Gatti
>
>  *
>
>     Richard H?chenberger
>
>  *
>
>     Robert Luke
>
>  *
>
>     Robert Oostenveld
>
>  *
>
>     Sebastian Major
>
>  *
>
>     Sophie Herbst
>
>  *
>
>     Stefan Appelhoff
>
>  *
>
>     Stefan Repplinger
>
>  *
>
>     Thomas Hartmann
>
>  *
>
>     Victor F?rat
>
>  *
>
>     Yu-Han Luo
>
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging


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From jbpoline at gmail.com  Sat Mar 28 18:33:11 2020
From: jbpoline at gmail.com (JB Poline)
Date: Sat, 28 Mar 2020 18:33:11 -0400
Subject: [Neuroimaging] [ANN] MNE-Python 0.20
In-Reply-To: <c9ee7953-a05c-bc7d-4fd0-c8304d897ef9@inria.fr>
References: <CADeotZpczGNBrpDNPAFUoj_k3nUcg4YR4ARWvcOFKQ5GzcDEeQ@mail.gmail.com>
 <c9ee7953-a05c-bc7d-4fd0-c8304d897ef9@inria.fr>
Message-ID: <CALMaa80f-hCjz0db7j62oKqMQeFzHyrWSYmz-GpF=K66xiAEFQ@mail.gmail.com>

congrats indeed!

On Sat, Mar 28, 2020 at 4:59 AM bthirion <bertrand.thirion at inria.fr> wrote:

> Congratulations for all the plotting improvements.
> B
>
> On 28/03/2020 09:47, Alexandre Gramfort wrote:
>
> Hi,
>
> First we hope that you?re safe in these troubled times.
>
> We are pleased to announce the new 0.20 release of MNE-Python (
> https://mne.tools/ <https://mne.tools/stable/index.html>)
>
> A few highlights
>
> ============
>
>    -
>
>    PyVista 0.24 is now available for 3D plotting (alternative to mayavi).
>    This is a big step forward for source space data visualization that allows
>    users to explore time interactively, pick vertices to view their time
>    activation courses, (auto-)adjust color scales, etc. To use it, `pip
>    install -U pyvista` and then in your Python script do
>    `mne.viz.set_3d_backend(?pyvista?)`. You should then be good to go: Simply
>    plot your source-time course data via stc.plot(), and the improved
>    interface should open automatically!
>    -
>
>    Automatic estimation of head motion from cHPI MEG coils in the
>    mne.chpi namespace.
>    -
>
>    Automatic detection of bad (flat or overly noisy) MEG channels via the
>    new find_bad_channels_maxwell function
>    -
>
>    New topography plotting code to take into account head position and
>    deal properly with channel subsets
>    -
>
>    New function and tutorial for estimating source-power from covariance
>    matrices using MNE (as commonly done with a beamformer).
>    -
>
>    Extensive improvements to the narrative documentation
>    https://mne.tools/stable/auto_tutorials/index.html
>
>
> Notable API changes
>
> ================
>
>    -
>
>    Sensors shown in relationship to a head circle, as in topomap
>    plotting, are now systematically converted from their given physical
>    locations. Using a static layout (such as those typically used with topo
>    plots) has been deprecated.
>
>
> For a full list of improvements and API changes, see:
>
> https://mne.tools/stable/whats_new.html#version-0-20
>
> To install the latest release the following command should do the job:
>
> pip install --upgrade --user mne
>
> As usual we welcome your bug reports, feature requests, critiques, and
>
> contributions.
>
> Some links:
>
> - https://github.com/mne-tools/mne-python (code + readme on how to
> install)
>
> - <http://martinos.org/mne/stable/>https://mne.tools/
> <https://mne.tools/stable/index.html> (full MNE documentation)
>
> Follow us on Twitter: https://twitter.com/mne_news
>
> Stay safe and take care !
>
> Regards,
>
> The MNE-Python developers
>
> People who contributed to this release (in alphabetical order):
>
>
>    -
>
>    Adam Li
>    -
>
>    Adonay Nunes
>    -
>
>    Alex Rockhill
>    -
>
>    Alexandre Gramfort
>    -
>
>    Ariel Rokem
>    -
>
>    Britta Westner
>    -
>
>    Carlos de la Torre
>    -
>
>    Christian Brodbeck
>    -
>
>    Christian O?Reilly
>    -
>
>    Chun-Hui Li
>    -
>
>    Clemens Brunner
>    -
>
>    Daniel McCloy
>    -
>
>    Demetres Kostas
>    -
>
>    Denis A. Engemann
>    -
>
>    Dmitrii Altukhov
>    -
>
>    Dominik Welke
>    -
>
>    Eric Larson
>    -
>
>    Ezequiel Mikulan
>    -
>
>    Fahimeh Mamashli
>    -
>
>    Fede Raimondo
>    -
>
>    Fu-Te Wong
>    -
>
>    Geoff Brookshire
>    -
>
>    Guillaume Favelier
>    -
>
>    Henrich Kolkhorst
>    -
>
>    Joan Massich
>    -
>
>    Jos? C. Garc?a Alanis
>    -
>
>    Jussi Nurminen
>    -
>
>    Kaisu Lankinen
>    -
>
>    Luke Bloy
>    -
>
>    Mainak Jas
>    -
>
>    Marijn van Vliet
>    -
>
>    Mathurin Massias
>    -
>
>    Mikolaj Magnuski
>    -
>
>    Mohamed Sherif
>    -
>
>    Mohammad Daneshzand
>    -
>
>    Nataliia Kozhemiako
>    -
>
>    Nicolas Barascud
>    -
>
>    Nicolas Legrand
>    -
>
>    Olaf Hauk
>    -
>
>    Padma Sundaram
>    -
>
>    Ramiro Gatti
>    -
>
>    Richard H?chenberger
>    -
>
>    Robert Luke
>    -
>
>    Robert Oostenveld
>    -
>
>    Sebastian Major
>    -
>
>    Sophie Herbst
>    -
>
>    Stefan Appelhoff
>    -
>
>    Stefan Repplinger
>    -
>
>    Thomas Hartmann
>    -
>
>    Victor F?rat
>    -
>
>    Yu-Han Luo
>
>
>
> _______________________________________________
> Neuroimaging mailing listNeuroimaging at python.orghttps://mail.python.org/mailman/listinfo/neuroimaging
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
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From anders.eklund at liu.se  Tue Mar 31 16:52:21 2020
From: anders.eklund at liu.se (Anders Eklund)
Date: Tue, 31 Mar 2020 20:52:21 +0000
Subject: [Neuroimaging] Nibabel error
Message-ID: <HE1P191MB02507A6D0A54609DD28D0BAB8EC80@HE1P191MB0250.EURP191.PROD.OUTLOOK.COM>

Hello,

I get this error when I'm trying to use nibabel (2.5.1 I think), has anyone seen it before?



In prepare_3d_tf_record_dataset

    img = nib.load(f)

  File "/home/andek67/.local/lib/python3.7/site-packages/nibabel/loadsave.py", line 47, in load

    is_valid, sniff = image_klass.path_maybe_image(filename, sniff)

  File "/home/andek67/.local/lib/python3.7/site-packages/nibabel/filebasedimages.py", line 500, in path_maybe_image

    klass._compressed_suffixes)

  File "/home/andek67/.local/lib/python3.7/site-packages/nibabel/filename_parser.py", line 265, in splitext_addext

    if endswith(filename, ext):

  File "/home/andek67/.local/lib/python3.7/site-packages/nibabel/filename_parser.py", line 223, in _iendswith

    return whole.lower().endswith(end.lower())

AttributeError: 'PosixPath' object has no attribute 'lower'

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From sulantha.s at gmail.com  Tue Mar 31 17:03:36 2020
From: sulantha.s at gmail.com (Sulantha Sanjeewa)
Date: Tue, 31 Mar 2020 14:03:36 -0700
Subject: [Neuroimaging] Nibabel error
In-Reply-To: <HE1P191MB02507A6D0A54609DD28D0BAB8EC80@HE1P191MB0250.EURP191.PROD.OUTLOOK.COM>
References: <HE1P191MB02507A6D0A54609DD28D0BAB8EC80@HE1P191MB0250.EURP191.PROD.OUTLOOK.COM>
Message-ID: <CAPM2tng+OH5CxxD4s6jUo327ZV60AyW_eLEnMk1ruxcJQ0j1fQ@mail.gmail.com>

Can you try 'f' as a string ? Instead of a PosixPath object?



On Tue, Mar 31, 2020, 2:00 PM Anders Eklund <anders.eklund at liu.se> wrote:

> Hello,
>
> I get this error when I'm trying to use nibabel (2.5.1 I think), has
> anyone seen it before?
>
>
> In prepare_3d_tf_record_dataset
>
>     img = nib.load(f)
>
>   File
> "/home/andek67/.local/lib/python3.7/site-packages/nibabel/loadsave.py",
> line 47, in load
>
>     is_valid, sniff = image_klass.path_maybe_image(filename, sniff)
>
>   File
> "/home/andek67/.local/lib/python3.7/site-packages/nibabel/filebasedimages.py",
> line 500, in path_maybe_image
>
>     klass._compressed_suffixes)
>
>   File
> "/home/andek67/.local/lib/python3.7/site-packages/nibabel/filename_parser.py",
> line 265, in splitext_addext
>
>     if endswith(filename, ext):
>
>   File
> "/home/andek67/.local/lib/python3.7/site-packages/nibabel/filename_parser.py",
> line 223, in _iendswith
>
>     return whole.lower().endswith(end.lower())
>
> AttributeError: 'PosixPath' object has no attribute 'lower'
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From anders.eklund at liu.se  Tue Mar 31 17:16:55 2020
From: anders.eklund at liu.se (Anders Eklund)
Date: Tue, 31 Mar 2020 21:16:55 +0000
Subject: [Neuroimaging] Nibabel error
In-Reply-To: <CAPM2tng+OH5CxxD4s6jUo327ZV60AyW_eLEnMk1ruxcJQ0j1fQ@mail.gmail.com>
References: <HE1P191MB02507A6D0A54609DD28D0BAB8EC80@HE1P191MB0250.EURP191.PROD.OUTLOOK.COM>,
 <CAPM2tng+OH5CxxD4s6jUo327ZV60AyW_eLEnMk1ruxcJQ0j1fQ@mail.gmail.com>
Message-ID: <HE1P191MB025026D45BAA5ECC6A7B32A88EC80@HE1P191MB0250.EURP191.PROD.OUTLOOK.COM>

That seems to work, thanks!
________________________________
From: Neuroimaging <neuroimaging-bounces+anders.eklund=liu.se at python.org> on behalf of Sulantha Sanjeewa <sulantha.s at gmail.com>
Sent: Tuesday, March 31, 2020 11:03 PM
To: Neuroimaging analysis in Python <neuroimaging at python.org>
Subject: Re: [Neuroimaging] Nibabel error

Can you try 'f' as a string ? Instead of a PosixPath object?



On Tue, Mar 31, 2020, 2:00 PM Anders Eklund <anders.eklund at liu.se<mailto:anders.eklund at liu.se>> wrote:
Hello,

I get this error when I'm trying to use nibabel (2.5.1 I think), has anyone seen it before?



In prepare_3d_tf_record_dataset

    img = nib.load(f)

  File "/home/andek67/.local/lib/python3.7/site-packages/nibabel/loadsave.py", line 47, in load

    is_valid, sniff = image_klass.path_maybe_image(filename, sniff)

  File "/home/andek67/.local/lib/python3.7/site-packages/nibabel/filebasedimages.py", line 500, in path_maybe_image

    klass._compressed_suffixes)

  File "/home/andek67/.local/lib/python3.7/site-packages/nibabel/filename_parser.py", line 265, in splitext_addext

    if endswith(filename, ext):

  File "/home/andek67/.local/lib/python3.7/site-packages/nibabel/filename_parser.py", line 223, in _iendswith

    return whole.lower().endswith(end.lower())

AttributeError: 'PosixPath' object has no attribute 'lower'

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