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Hi,
We run freesurfer 6 on an HPC environment. We received this error when trying to run an asegstats2table script:
[jabsher@node0130 results]$ ./asegstats2table_scr File "/zfs/hpcnirc/usr/bin/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax File "/zfs/hpcnirc/usr/bin/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax [jabsher@node0130 results]$
We are running this version: You are running this version of FreeSurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Here are the loaded modules: Currently Loaded Modules: 1) libxml2/2.9.10-gcc/8.3.1 2) openblas/0.3.10-gcc/8.3.1 3) matlab/2021b 4) anaconda3/5.1.0-gcc/8.3.1 5) openmpi/3.1.6-gcc/8.3.1-cuda10_2-ucx 6) cuda/10.2.89-gcc/8.4.1
The script is attached.
We've gone to the wiki page (asegstats2table - Free Surfer Wiki (harvard.edu)https://secure-web.cisco.com/1eU_J79ltbqe0p9Duk2YmurJuRaHFOpDSqizGlzIClXlSHNDoX01peVPjCFssUOA3Mlb1quthTsKUOfwS65KSww69BVSi4WssLubqfwojanbJzn-txjP9a9dcTomTOV47KEO0yipyn-gnMGh5mQc2nBSnbXc_JNClpRWtfC1J2Sop4yZHPaYE92ZUl5HfmMDILQnf83VYL_C-Cavmj6n8fGo9WczFU394e19usu80uYI_hQzzkzJg185KV2k_S54OlGfGXdu7wD2uN4b430Gi-LCfT5Al1pK98T5MuwWv_bfGXWxOH6MAGE-4ViTJD4OV/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fasegstats2table and tried essentially all permutations, including specifying the aseg.stats files by name for each subject. The "use -subjects" error comes up every time, and we tried this as specified, with -subjects followed by all the directory/subject names, with a \ at the end of each line for readability.
I know this must be something very straightforward, but hoping you can help. Thanks,
Warm Regards,
John R. Absher, MD, FAAN Associate Professor, University of South Carolina School of Medicine Greenville Department of Internal Medicine, Division of Neurology Clinical Assistant Professor, Clemson University School of Health Research (CUSHR) Graduate Faculty, Clemson University School of Public Health Sciences Prisma Health-Upstate 200 Patewood Drive, Suite 350B Greenville, SC 29615 John.Absher@prismahealth.orgmailto:John.Absher@prismahealth.org or absher@mailbox.sc.edumailto:absher@mailbox.sc.edu or jabsher@clemson.edumailto:jabsher@clemson.edu 864-454-4500 (office) 864-350-6655 (mobile) 864-454-4505 (fax)
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