From garyfallidis at gmail.com  Wed Sep  8 17:27:03 2021
From: garyfallidis at gmail.com (Eleftherios Garyfallidis)
Date: Wed, 8 Sep 2021 17:27:03 -0400
Subject: [Neuroimaging] [DIPY] Shared calendar and open meetings
Message-ID: <CAN6JmWOyrZnDAK62dP6SKe_U8ufCV7YOt=eA33HQFJpMsafE5Q@mail.gmail.com>

Hello all,

The DIPY open meetings are starting again tomorrow Sep 9 at 1pm EST / 7pm
CET / 10am PT.
The meetings will be repeated every 2 weeks, usually at the same time.
These open meetings include presentations on novel imaging methods or
discussions about DIPY's upcoming features.

More information about these events you can find in the link below:

https://github.com/dipy/dipy/discussions/2398

To be always updated with the latest events you can include the DIPY
calendar
<https://calendar.google.com/calendar/u/0?cid=dXY4YzUwZmtmdnM1Mjk4MzdrMjk4dWVxaDBAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ>
which provides
information about upcoming meetings, talks, workshops and sprints.

Note that on September 23rd, Jens Sj?lund will talk about the excellent
topic of Bayesian Uncertainty Quantification to improve model fitting.

Best regards,
Eleftherios
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From abdou at stanford.edu  Sat Sep 11 20:07:41 2021
From: abdou at stanford.edu (Abdou Thiam)
Date: Sun, 12 Sep 2021 00:07:41 +0000
Subject: [Neuroimaging] Postdoctoral Fellow Position in Simultaneous Spinal
 Cord-Brain fMRI
In-Reply-To: <BYAPR02MB4853537C9D255E11D5A67A50CAD89@BYAPR02MB4853.namprd02.prod.outlook.com>
References: <BYAPR02MB48531CE0DE2B73035B8906DDCAD79@BYAPR02MB4853.namprd02.prod.outlook.com>
 <BYAPR02MB4853537C9D255E11D5A67A50CAD89@BYAPR02MB4853.namprd02.prod.outlook.com>
Message-ID: <BYAPR02MB4853C3DBDAFFC20397CF9FB5CAD89@BYAPR02MB4853.namprd02.prod.outlook.com>



Abdou Thiam

Clinical Research Coordinator

Stanford University School of Medicine

Department of Anesthesiology, Perioperative and Pain Medicine

Division of Pain Medicine

Stanford Systems Neuroscience and Pain Lab

1070 Arastradero Road, Suite 200, MC 5596

Palo Alto, CA 94304

Phone: (650) -721-4016 | Fax: (650) -725-9642

[cid:image001.jpg at 01D38AB2.52B03DD0]
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From reine097 at umn.edu  Tue Sep 28 10:07:37 2021
From: reine097 at umn.edu (Paul Reiners)
Date: Tue, 28 Sep 2021 09:07:37 -0500
Subject: [Neuroimaging] nibabel.filebasedimages.ImageFileError for large
 label files
Message-ID: <CAEqJVpPPs1=svFwbLVbrW=0Gfv13BBPgouc8aaUVNGwZS_S=Zw@mail.gmail.com>

I am getting the following error when loading a large labeled NIFTI file of
size 14.4 MB.

    Traceback (most recent call last):
      File
"/home/miran045/reine097/projects2/lab2im/lab2im/dcan/reproduce_load_error.py",
line 7, in <module>
        img = nib.load(file_path)
      File
"/home/miran045/reine097/.local/lib/python3.7/site-packages/nibabel/loadsave.py",
line 55, in load
        raise ImageFileError(f'Cannot work out file type of "{filename}"')
    nibabel.filebasedimages.ImageFileError: Cannot work out file type of
"/home/feczk001/shared/data/nnUNet/nnUNet_raw_data_base/nnUNet_raw_data/Task509_Paper/labelsTr1/1mo_sub-375518.nii.gz"

Here is the code:

    import nibabel as nib

    print(nib.__version__)

    file_path =
'/home/feczk001/shared/data/nnUNet/nnUNet_raw_data_base/nnUNet_raw_data/Task509_Paper/labelsTr1/1mo_sub'
\
                '-375518.nii.gz'
    img = nib.load(file_path)
    print(img.shape)

This does not happen when I try to open such files of smaller size (on the
order of KB).  I can open this file in FreeSurfer FreeView without error
and it looks fine.  This is happening with version 3.2.1 of NiBabel.
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From markiewicz at stanford.edu  Tue Sep 28 11:17:57 2021
From: markiewicz at stanford.edu (Christopher Markiewicz)
Date: Tue, 28 Sep 2021 15:17:57 +0000
Subject: [Neuroimaging] nibabel.filebasedimages.ImageFileError for large
 label files
In-Reply-To: <CAEqJVpPPs1=svFwbLVbrW=0Gfv13BBPgouc8aaUVNGwZS_S=Zw@mail.gmail.com>
References: <CAEqJVpPPs1=svFwbLVbrW=0Gfv13BBPgouc8aaUVNGwZS_S=Zw@mail.gmail.com>
Message-ID: <MN2PR02MB67529816528BCC6309D89C61A9A89@MN2PR02MB6752.namprd02.prod.outlook.com>

Hi Paul,

Is it possible that the file is not actually gzipped? This is the most common cause of this error that I've seen.

Best,
Chris

________________________________________
From: Neuroimaging <neuroimaging-bounces+markiewicz=stanford.edu at python.org> on behalf of Paul Reiners via Neuroimaging <neuroimaging at python.org>
Sent: Tuesday, September 28, 2021 10:07
To: neuroimaging at python.org
Cc: Paul Reiners
Subject: [Neuroimaging] nibabel.filebasedimages.ImageFileError for large label files

I am getting the following error when loading a large labeled NIFTI file of size 14.4 MB.

    Traceback (most recent call last):
      File "/home/miran045/reine097/projects2/lab2im/lab2im/dcan/reproduce_load_error.py", line 7, in <module>
        img = nib.load(file_path)
      File "/home/miran045/reine097/.local/lib/python3.7/site-packages/nibabel/loadsave.py", line 55, in load
        raise ImageFileError(f'Cannot work out file type of "{filename}"')
    nibabel.filebasedimages.ImageFileError: Cannot work out file type of "/home/feczk001/shared/data/nnUNet/nnUNet_raw_data_base/nnUNet_raw_data/Task509_Paper/labelsTr1/1mo_sub-375518.nii.gz"

Here is the code:

    import nibabel as nib

    print(nib.__version__)

    file_path = '/home/feczk001/shared/data/nnUNet/nnUNet_raw_data_base/nnUNet_raw_data/Task509_Paper/labelsTr1/1mo_sub' \
                '-375518.nii.gz'
    img = nib.load(file_path)
    print(img.shape)

This does not happen when I try to open such files of smaller size (on the order of KB).  I can open this file in FreeSurfer FreeView without error and it looks fine.  This is happening with version 3.2.1 of NiBabel.


From willtironedev at gmail.com  Tue Sep 28 12:13:16 2021
From: willtironedev at gmail.com (Will Tirone)
Date: Tue, 28 Sep 2021 12:13:16 -0400
Subject: [Neuroimaging] hello!
Message-ID: <CA+jBUMx1T4Juh6yaCFP9SfmCigjbf2cov52bJriFpjk-3+DbXA@mail.gmail.com>

Hi all,

This is Will Tirone, I recently found the NiPy package and would like to
contribute. I have made a few contributions to SciPy in the past, and I am
reading through the developer guidelines for NiPy now.

If there are any low-hanging fruit bug fixes that need attention, please
let me know. Otherwise, I will keep an eye on the issues page on GitHub for
some good first timer issues.

Best,
Will
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From reine097 at umn.edu  Tue Sep 28 13:23:16 2021
From: reine097 at umn.edu (Paul Reiners)
Date: Tue, 28 Sep 2021 12:23:16 -0500
Subject: [Neuroimaging] nibabel.filebasedimages.ImageFileError for large
 label files
In-Reply-To: <MN2PR02MB67529816528BCC6309D89C61A9A89@MN2PR02MB6752.namprd02.prod.outlook.com>
References: <CAEqJVpPPs1=svFwbLVbrW=0Gfv13BBPgouc8aaUVNGwZS_S=Zw@mail.gmail.com>
 <MN2PR02MB67529816528BCC6309D89C61A9A89@MN2PR02MB6752.namprd02.prod.outlook.com>
Message-ID: <CAEqJVpN8uK2G-jegss_VokXhdKF9uYHKzrcQop30Gz3Raiwz9A@mail.gmail.com>

Hi Chris,

Yes, that was the problem.  Thanks!

Paul


On Tue, Sep 28, 2021 at 11:12 AM Christopher Markiewicz <
markiewicz at stanford.edu> wrote:

> Hi Paul,
>
> Is it possible that the file is not actually gzipped? This is the most
> common cause of this error that I've seen.
>
> Best,
> Chris
>
> ________________________________________
> From: Neuroimaging <neuroimaging-bounces+markiewicz=
> stanford.edu at python.org> on behalf of Paul Reiners via Neuroimaging <
> neuroimaging at python.org>
> Sent: Tuesday, September 28, 2021 10:07
> To: neuroimaging at python.org
> Cc: Paul Reiners
> Subject: [Neuroimaging] nibabel.filebasedimages.ImageFileError for large
> label files
>
> I am getting the following error when loading a large labeled NIFTI file
> of size 14.4 MB.
>
>     Traceback (most recent call last):
>       File
> "/home/miran045/reine097/projects2/lab2im/lab2im/dcan/reproduce_load_error.py",
> line 7, in <module>
>         img = nib.load(file_path)
>       File
> "/home/miran045/reine097/.local/lib/python3.7/site-packages/nibabel/loadsave.py",
> line 55, in load
>         raise ImageFileError(f'Cannot work out file type of "{filename}"')
>     nibabel.filebasedimages.ImageFileError: Cannot work out file type of
> "/home/feczk001/shared/data/nnUNet/nnUNet_raw_data_base/nnUNet_raw_data/Task509_Paper/labelsTr1/1mo_sub-375518.nii.gz"
>
> Here is the code:
>
>     import nibabel as nib
>
>     print(nib.__version__)
>
>     file_path =
> '/home/feczk001/shared/data/nnUNet/nnUNet_raw_data_base/nnUNet_raw_data/Task509_Paper/labelsTr1/1mo_sub'
> \
>                 '-375518.nii.gz'
>     img = nib.load(file_path)
>     print(img.shape)
>
> This does not happen when I try to open such files of smaller size (on the
> order of KB).  I can open this file in FreeSurfer FreeView without error
> and it looks fine.  This is happening with version 3.2.1 of NiBabel.
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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