Can you check if you have any extra empty lines after your last ‘Input’?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Laura Willers de Souza Sent: Thursday, December 14, 2023 3:16 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] aparcstats2table - IndexError
External Email - Use Caution Hello FreeSurfer Developers, I'm trying to get the cortical thickness values for a list of subjects using aparcstats2table and I'm encountering this error:
aparcstats2table --fsgd subjects.test1.fsgd --meas thickness --hemi lh --common-parcs --tablefile lh.aparc.thickness.table SUBJECTS_DIR : /mnt/wsl/PHYSICALDRIVE1/FS_OUTPUTS Traceback (most recent call last): File "/usr/local/freesurfer/7.4.1/python/scripts/aparcstats2table", line 376, in <module> subj_listoftuples = assemble_inputs(options) File "/usr/local/freesurfer/7.4.1/python/scripts/aparcstats2table", line 273, in assemble_inputs if splitline[0].upper() == 'INPUT': IndexError: list index out of range
The fsgd file only contains the list of subjects, as illustrated below: GroupDescriptorFile 1 Title subjects.test1 Input 002_S_0295_S13408 Input 002_S_0413_S13893 Input 002_S_0559_S14875
I have successfully executed the same command for an individual subject. For other measurements (surface area, volume) this error also occurs.
It's worth noting that the images and files for the subjects and recon-all are stored on an external hard drive that I have mounted on Linux, emulated on Windows. Could this be the source of the problem?
I appreciate any assistance you can provide with resolving this issue.
Thanks in advance!
Laura Willers de Souza
PhD Student in Pharmacology and Therapeutics
Zimmer Lab - Federal University of Rio Grande do Sul
- Porto Alegre/RS - Brazil