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

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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