I am also attaching the new core.py with the bug fix. You can unzip and copy it to $FREESURFER/python/gems/subregions
Best, Avnish ________________________________ From: Kumar, Avnish Avnish.Kumar@MGH.HARVARD.EDU Sent: Friday, September 23, 2022 11:47 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: Nolan, Jackson JNOLAN5@mgh.harvard.edu; mdalaminbadal@gmail.com mdalaminbadal@gmail.com Subject: Re: [Freesurfer] segment_subregions failed
Hi Markus,
This bug has been fixedhttps://github.com/freesurfer/freesurfer/commit/9af3deaaf8aa44500b8ccf136179afe8c003a172 in the dev branch of Freesurfer (FS). You can get the changes in your local copy of FS by either git checkout the python/gems/subregions/core.py file into the appropriate subfolder (<FS_install_dir>/python/gems/subregions) where you installed FS or you could simply edit the core.py file at that location as in the bug fixhttps://github.com/freesurfer/freesurfer/commit/9af3deaaf8aa44500b8ccf136179afe8c003a172.
Best, Avnish ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Markus Handal Sneve m.h.sneve@psykologi.uio.no Sent: Wednesday, September 21, 2022 2:35 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: Nolan, Jackson JNOLAN5@mgh.harvard.edu; mdalaminbadal@gmail.com mdalaminbadal@gmail.com Subject: Re: [Freesurfer] segment_subregions failed
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Hi,
Sorry if this ends up in the wrong place, had to reactivate my FS-mailing list account.
So I get the exact same error as reported by Mamun Al-Amin when running segment_subregion (FS v7.3.2).
Fresh terminal, no other FS version running in the background, build-stamp.txt shows the correct version.
Hopefully you can see the screenshot below, sadly cannot ctrl-c text out of our cluster
[cid:02AE0EFB-80BC-4895-B44D-AC05CB77D890]
Thanks!
Markus Handal Sneve, Ph.D. Center for Lifespan Changes in Brain and Cognition Department of Psychology University of Oslo
