From markiewicz at stanford.edu  Wed Apr  1 08:28:17 2020
From: markiewicz at stanford.edu (Christopher Markiewicz)
Date: Wed, 1 Apr 2020 12:28:17 +0000
Subject: [Neuroimaging] Nibabel error
In-Reply-To: <HE1P191MB02507A6D0A54609DD28D0BAB8EC80@HE1P191MB0250.EURP191.PROD.OUTLOOK.COM>
References: <HE1P191MB02507A6D0A54609DD28D0BAB8EC80@HE1P191MB0250.EURP191.PROD.OUTLOOK.COM>
Message-ID: <MN2PR02MB6752AA5B5986AAF248649E15A9C90@MN2PR02MB6752.namprd02.prod.outlook.com>

Support for os.PathLike objects was added in nibabel 3.0. Please let us know if you find a case that fails in that version or later.
________________________________
From: Neuroimaging <neuroimaging-bounces+markiewicz=stanford.edu at python.org> on behalf of Anders Eklund <anders.eklund at liu.se>
Sent: Tuesday, March 31, 2020 4:52 PM
To: neuroimaging at python.org <neuroimaging at python.org>
Subject: [Neuroimaging] Nibabel error

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 markiewicz at stanford.edu  Mon Apr 20 09:25:08 2020
From: markiewicz at stanford.edu (Christopher Markiewicz)
Date: Mon, 20 Apr 2020 13:25:08 +0000
Subject: [Neuroimaging] ANN: NiBabel 3.1.0 and 2.5.2
Message-ID: <MN2PR02MB6752BFA1B61E684C72CD634AA9D70@MN2PR02MB6752.namprd02.prod.outlook.com>

Hi all,

NiBabel 3.1.0 is out. This release completes a conversion from nose to pytest, ensuring Python 3.9 compatibility when that comes out later this year. Additionally, we added some conformation tools as both a Python function and a new nib-conform command-line interface.

NiBabel 2.5.2 was released about two weeks ago, an update in the 2.5.x series that retains support for Python 2.7 and 3.4. A couple fixes for SyntaxWarnings were back-ported, but the main change was setting maximum compatible versions for numpy and scipy to 1.16.x and 1.2.x, which are respectively the final series with Python 2 support in those projects. Python 3 users who want to use newer features of numpy and scipy are encouraged to upgrade to NiBabel 3.

Particular thanks to the team that sprinted on tests in February (Dorota Jarecka, Roberto Guidotti, Anibal Solon, and Or Duek). And thanks as usual to everyone who's contributed, submitted bug reports or fixes.

Please cite NiBabel 2.5.2 using the Zenodo archive: https://doi.org/10.5281/zenodo.3745545
Please cite NiBabel 3.1.0 using the Zenodo archive: https://doi.org/10.5281/zenodo.3757992

I hope everybody is staying well.

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, Stephan Gerhard and Ross Markello (RM).

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

3.1.0 (Monday 20 April 2020)
============================

New feature release in the 3.1.x series.

New features
------------
* Conformation function (``processing.conform``) and CLI tool
  (``nib-conform``) to apply shape, orientation and zooms (pr/853) (Jakub
  Kaczmarzyk, reviewed by CM, YOH)
* Affine rescaling function (``affines.rescale_affine``) to update
  dimensions and voxel sizes (pr/853) (CM, reviewed by Jakub Kaczmarzyk)

Bug fixes
---------
* Delay import of h5py until neded (pr/889) (YOH, reviewed by CM)

Maintenance
-----------
* Fix typo in documentation (pr/893) (Zvi Baratz, reviewed by CM)
* Tests converted from nose to pytest (pr/865 + many sub-PRs)
  (Dorota Jarecka, Krzyzstof Gorgolewski, Roberto Guidotti, Anibal Solon,
  Or Duek, CM)

API changes and deprecations
----------------------------
* ``kw_only_meth``/``kw_only_func`` decorators are deprecated (pr/848)
  (RM, reviewed by CM)


2.5.2 (Wednesday 8 April 2020)
==============================

Bug-fix release in the 2.5.x series. This is an extended-support series,
providing bug fixes for Python 2.7 and 3.4.

This and all future releases in the 2.5.x series will be incompatible with
Python 3.9. The last compatible series of numpy and scipy are 1.16.x and
1.2.x, respectively.

If you are able to upgrade to Python 3, it is recommended to upgrade to
NiBabel 3.

Bug fixes
---------
* Change strings with invalid escapes to raw strings (pr/827) (EL, reviewed
  by CM)
* Re-import externals/netcdf.py from scipy to resolve numpy deprecation
  (pr/821) (CM)

Maintenance
-----------
* Set maximum numpy to 1.16.x, maximum scipy to 1.2.x (pr/901) (CM)


--

Chris Markiewicz

Center for Reproducible Neuroscience

Stanford University
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From bertrand.thirion at inria.fr  Mon Apr 20 10:26:44 2020
From: bertrand.thirion at inria.fr (Bertrand Thirion)
Date: Mon, 20 Apr 2020 16:26:44 +0200 (CEST)
Subject: [Neuroimaging] ANN: NiBabel 3.1.0 and 2.5.2
In-Reply-To: <MN2PR02MB6752BFA1B61E684C72CD634AA9D70@MN2PR02MB6752.namprd02.prod.outlook.com>
References: <MN2PR02MB6752BFA1B61E684C72CD634AA9D70@MN2PR02MB6752.namprd02.prod.outlook.com>
Message-ID: <82440286.26284536.1587392804583.JavaMail.zimbra@inria.fr>

Congratulations for the release ! and thx ! 

Bertrand 

> De: "Christopher Markiewicz" <markiewicz at stanford.edu>
> ?: "Neuroimaging analysis in Python" <neuroimaging at python.org>
> Envoy?: Lundi 20 Avril 2020 15:25:08
> Objet: [Neuroimaging] ANN: NiBabel 3.1.0 and 2.5.2

> Hi all,

> NiBabel 3.1.0 is out. This release completes a conversion from nose to pytest,
> ensuring Python 3.9 compatibility when that comes out later this year.
> Additionally, we added some conformation tools as both a Python function and a
> new nib-conform command-line interface.

> NiBabel 2.5.2 was released about two weeks ago, an update in the 2.5.x series
> that retains support for Python 2.7 and 3.4. A couple fixes for SyntaxWarnings
> were back-ported, but the main change was setting maximum compatible versions
> for numpy and scipy to 1.16.x and 1.2.x, which are respectively the final
> series with Python 2 support in those projects. Python 3 users who want to use
> newer features of numpy and scipy are encouraged to upgrade to NiBabel 3.

> Particular thanks to the team that sprinted on tests in February (Dorota
> Jarecka, Roberto Guidotti, Anibal Solon, and Or Duek). And thanks as usual to
> everyone who's contributed, submitted bug reports or fixes.

> Please cite NiBabel 2.5.2 using the Zenodo archive: [
> https://doi.org/10.5281/zenodo.3745545 |
> https://doi.org/10.5281/zenodo.3745545 ]
> Please cite NiBabel 3.1.0 using the Zenodo archive: [
> https://doi.org/10.5281/zenodo.3757992 |
> https://doi.org/10.5281/zenodo.3757992 ]

> I hope everybody is staying well.

> 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, Stephan Gerhard and Ross Markello (RM).

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

> 3.1.0 (Monday 20 April 2020)
> ============================

> New feature release in the 3.1.x series.

> New features
> ------------
> * Conformation function (``processing.conform``) and CLI tool
> (``nib-conform``) to apply shape, orientation and zooms (pr/853) (Jakub
> Kaczmarzyk, reviewed by CM, YOH)
> * Affine rescaling function (``affines.rescale_affine``) to update
> dimensions and voxel sizes (pr/853) (CM, reviewed by Jakub Kaczmarzyk)

> Bug fixes
> ---------
> * Delay import of h5py until neded (pr/889) (YOH, reviewed by CM)

> Maintenance
> -----------
> * Fix typo in documentation (pr/893) (Zvi Baratz, reviewed by CM)
> * Tests converted from nose to pytest (pr/865 + many sub-PRs)
> (Dorota Jarecka, Krzyzstof Gorgolewski, Roberto Guidotti, Anibal Solon,
> Or Duek, CM)

> API changes and deprecations
> ----------------------------
> * ``kw_only_meth``/``kw_only_func`` decorators are deprecated (pr/848)
> (RM, reviewed by CM)

> 2.5.2 (Wednesday 8 April 2020)
> ==============================

> Bug-fix release in the 2.5.x series. This is an extended-support series,
> providing bug fixes for Python 2.7 and 3.4.

> This and all future releases in the 2.5.x series will be incompatible with
> Python 3.9. The last compatible series of numpy and scipy are 1.16.x and
> 1.2.x, respectively.

> If you are able to upgrade to Python 3, it is recommended to upgrade to
> NiBabel 3.

> Bug fixes
> ---------
> * Change strings with invalid escapes to raw strings (pr/827) (EL, reviewed
> by CM)
> * Re-import externals/netcdf.py from scipy to resolve numpy deprecation
> (pr/821) (CM)

> Maintenance
> -----------
> * Set maximum numpy to 1.16.x, maximum scipy to 1.2.x (pr/901) (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 jbpoline at gmail.com  Tue Apr 21 10:51:46 2020
From: jbpoline at gmail.com (JB Poline)
Date: Tue, 21 Apr 2020 10:51:46 -0400
Subject: [Neuroimaging] ANN: NiBabel 3.1.0 and 2.5.2
In-Reply-To: <82440286.26284536.1587392804583.JavaMail.zimbra@inria.fr>
References: <MN2PR02MB6752BFA1B61E684C72CD634AA9D70@MN2PR02MB6752.namprd02.prod.outlook.com>
 <82440286.26284536.1587392804583.JavaMail.zimbra@inria.fr>
Message-ID: <CALMaa83BFRX_zmm8xc2z205yYhgEEnk=-Hr7YU=LVHAfxWJEpg@mail.gmail.com>

Ditto - thanks so much !

On Mon, Apr 20, 2020 at 10:28 AM Bertrand Thirion <bertrand.thirion at inria.fr>
wrote:

> Congratulations for the release ! and thx !
>
> Bertrand
>
>
> ------------------------------
>
> *De: *"Christopher Markiewicz" <markiewicz at stanford.edu>
> *?: *"Neuroimaging analysis in Python" <neuroimaging at python.org>
> *Envoy?: *Lundi 20 Avril 2020 15:25:08
> *Objet: *[Neuroimaging] ANN: NiBabel 3.1.0 and 2.5.2
>
> Hi all,
>
> NiBabel 3.1.0 is out. This release completes a conversion from nose to
> pytest, ensuring Python 3.9 compatibility when that comes out later this
> year. Additionally, we added some conformation tools as both a Python
> function and a new nib-conform command-line interface.
>
> NiBabel 2.5.2 was released about two weeks ago, an update in the 2.5.x
> series that retains support for Python 2.7 and 3.4. A couple fixes for
> SyntaxWarnings were back-ported, but the main change was setting maximum
> compatible versions for numpy and scipy to 1.16.x and 1.2.x, which are
> respectively the final series with Python 2 support in those projects.
> Python 3 users who want to use newer features of numpy and scipy are
> encouraged to upgrade to NiBabel 3.
>
> Particular thanks to the team that sprinted on tests in February (Dorota
> Jarecka, Roberto Guidotti, Anibal Solon, and Or Duek). And thanks as usual
> to everyone who's contributed, submitted bug reports or fixes.
>
> Please cite NiBabel 2.5.2 using the Zenodo archive:
> https://doi.org/10.5281/zenodo.3745545
> Please cite NiBabel 3.1.0 using the Zenodo archive:
> https://doi.org/10.5281/zenodo.3757992
>
> I hope everybody is staying well.
>
> 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, Stephan Gerhard and Ross Markello
> (RM).
>
> References like "pr/298" refer to github pull request numbers.
>
> 3.1.0 (Monday 20 April 2020)
> ============================
>
> New feature release in the 3.1.x series.
>
> New features
> ------------
> * Conformation function (``processing.conform``) and CLI tool
>   (``nib-conform``) to apply shape, orientation and zooms (pr/853) (Jakub
>   Kaczmarzyk, reviewed by CM, YOH)
> * Affine rescaling function (``affines.rescale_affine``) to update
>   dimensions and voxel sizes (pr/853) (CM, reviewed by Jakub Kaczmarzyk)
>
> Bug fixes
> ---------
> * Delay import of h5py until neded (pr/889) (YOH, reviewed by CM)
>
> Maintenance
> -----------
> * Fix typo in documentation (pr/893) (Zvi Baratz, reviewed by CM)
> * Tests converted from nose to pytest (pr/865 + many sub-PRs)
>   (Dorota Jarecka, Krzyzstof Gorgolewski, Roberto Guidotti, Anibal Solon,
>   Or Duek, CM)
>
> API changes and deprecations
> ----------------------------
> * ``kw_only_meth``/``kw_only_func`` decorators are deprecated (pr/848)
>   (RM, reviewed by CM)
>
>
> 2.5.2 (Wednesday 8 April 2020)
> ==============================
>
> Bug-fix release in the 2.5.x series. This is an extended-support series,
> providing bug fixes for Python 2.7 and 3.4.
>
> This and all future releases in the 2.5.x series will be incompatible with
> Python 3.9. The last compatible series of numpy and scipy are 1.16.x and
> 1.2.x, respectively.
>
> If you are able to upgrade to Python 3, it is recommended to upgrade to
> NiBabel 3.
>
> Bug fixes
> ---------
> * Change strings with invalid escapes to raw strings (pr/827) (EL, reviewed
>   by CM)
> * Re-import externals/netcdf.py from scipy to resolve numpy deprecation
>   (pr/821) (CM)
>
> Maintenance
> -----------
> * Set maximum numpy to 1.16.x, maximum scipy to 1.2.x (pr/901) (CM)
>
> --
>
> Chris Markiewicz
>
> Center for Reproducible Neuroscience
>
> Stanford University
>
> _______________________________________________
> 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 seralouk at hotmail.com  Fri Apr 24 07:57:50 2020
From: seralouk at hotmail.com (serafim loukas)
Date: Fri, 24 Apr 2020 11:57:50 +0000
Subject: [Neuroimaging] Yeo 17 brain parcellation - network names/ labels
In-Reply-To: <33F8B584-826B-4FD9-8EA1-C6F1DE4AB324@hotmail.com>
References: <33F8B584-826B-4FD9-8EA1-C6F1DE4AB324@hotmail.com>
Message-ID: <CFC95885-2919-4FBF-BC73-B049DE405180@hotmail.com>

Dear Neuroimaging in Python community,


I am trying to find the network labels (names) of the Yeo 17 brain parcellation.

I have used the function datasets.fetch_atlas_yeo_2011()  to download the Yeo atlas nifty files from http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011 as stated in the documentation (https://nilearn.github.io/modules/generated/nilearn.datasets.fetch_atlas_yeo_2011.html#nilearn.datasets.fetch_atlas_yeo_2011).

For the 7 network parcellation, the networks names can be easily found online however, I am not able to find the correct naming order for the 17 networks parcellation.

Do you know where I could find this information?


Bests,
Makis


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