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Hi there,

Something is odd with the path to your data (in red below):

/apps/freesurfer/7.0.0/freesurfer/subjects/APC011/stats/aseg.stats

Check your script/code and see where you have the path written out. If you delete the word above, it should work.

Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR/MSFHR Postdoctoral Research Fellow Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon

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On Apr 24, 2021, at 5:37 PM, Haneen Hakeem haneen.fahadh@gmail.com wrote:

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External Email - Use Caution

Hello FreeSurfer Developers,

I’m attempting to output stat files using “asegstats2table” and “aparcstats2table” but for some of my subjects I get the following error when I run the commands:

ERROR: Cannot find stats file /apps/freesurfer/7.0.0/freesurfer/subjects/APC011/stats/aseg.stats

However, when I check the stats file in FreeSurfer output directory, the stats files are there (including asset.stats). This issue is recurring with all “asegstats2table” and “aparcstats2table” stat files.

1) freesurfer version FreeSurfer 7.0 2) Platform: Bash remotely through High Performance Computing (HPC) on a MacOS Mojave 3) recon all log attached <recon-all.log>