External Email - Use Caution
Andrew,
That was very helpful.
Thank you!
J.
On Fri, Jan 3, 2020 at 5:02 PM Hoopes, Andrew <ahoo...@mgh.harvard.edu>
wrote:
> Hey Josh,
>
> Thanks for bringing this to our attention. This newline, which was always
> ignored by our surface reading utils, was inadvertently removed after a
> large refactor of the codebase (moving to c++). This is an innocuous change
> except for the fact that it, of course, breaks external surface readers
> like nibabel. I just fixed this in the development version so that the
> extra newline is once again included in surface files. If you're having
> trouble reading a surface in nibabel, with the fixed version, you could
> just do...
>
> mris_convert lh.surface lh.surface
>
> ...to save it correctly. The centos7 dev release has been updated with
> this fix, but you will have to wait until tomorrow for the centos6 release
> to rebuild.
>
> Best,
> Andrew
>
> ________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Joshua Jacobs <
> joshuajac...@flywheel.io>
> Sent: Thursday, January 2, 2020 2:06 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] Surface file format differences
>
> External Email - Use Caution
>
> Hello,
>
> When working with the nightly development version of FreeSurfer recon-all
> (freesurfer-linux-centos6_x86_64-dev.tar.gz 23-Dec-2019 06:01)
>
> The surface file format differed by one character (\n) from previous
> versions. What makes me suspicious of this change is the difference between
> output and the fsaverage subject. See head -n 3 surf/rh.white for each
> below.
>
> recon-all output:
> ���created by root on Tue Dec 31 23:05:44 2019
> ���YcR@��]�zk=�}���m�K�4�F���h��{yM��������0@
> �(��ě��̫�VY�vտ�1G�s��@t�4�*��>���C80�d?f���5��˿O+@�H&�fˍ����ο�\i�.3��I�
> ^���dn���ٿp�7_��:�x����)��!�o���
>
> fsaverage:
> ���created by greve on Thu Jul 19 12:52:07 2018
>
> �A�3^�f�Bp�nA�
>
> This is the case for all sample data in the FS/subjects/ directory save
> for "bert". The data of which had been produced on 2019-12.21.
>
> Although I have not tried freeview on these files, it fails to open in the
> python library nibabel.freesurfer.io.load_geometry.
>
> Is this change intended?
>
> Thank You.
>
> Josh J.
>
>
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