[FieldTrip] Help Running ft_postfreesurferscript.sh

[Schoffelen, J.M. (Jan Mathijs)]

Hi Michael,

The error suggests that an expected file is missing. Could it be that freesurfer produced incomplete output? (in other words: do you get an error only for this particular subject?)
If you don’t need the sulc/curv/thickness information, you can also try and bypass this error by commenting out the respective lines of code in the bash-script (including the lines that rely on using the newly create .gii files of those metrics).

Best wishes,
Jan-Mathijs

On 8 May 2025, at 15:37, Michael Houston via fieldtrip <fieldtrip at science.ru.nl> wrote:

Hi, everyone! I am trying to create a cortical sheet source model from the standard colin27 brain with accompanying DKT atlas for EEG source reconstruction (single_subj.nii in Fieldtrip template directory). After doing recon-all in FreeSurfer, the resulting meshes are far too large ~160k vertices per hemisphere which is taking too long to run the source analysis on. I followed the instructions according to this tutorial (https://www.fieldtriptoolbox.org/tutorial/source/sourcemodel/<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Fsource%2Fsourcemodel%2F&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C56b87b4413844102cc2e08dd93baa818%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638829152062216273%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=9SW8PMVRbQq5pZlyYdFH2lkvizm907sAAxpFQk5qRp4%3D&reserved=0>) and set up the HCP-Workbench and copied the requested directory contents to a common folder to use ft_postfreesurferscript.sh to make the lower resolution cortical meshes.

While I can get the script to run, I am facing the output and error copied below. If there is any other information I should provide please let me know. I am confused about this output because it looks like the error file is one that should be created by the script however it is not found. I would greatly appreciate any insight on how to fix this.:

Command
--------------
/mnt/c/Users/mjame/Documents/MATLAB/fieldtrip-20240504/bin/ft_postfreesurferscript.sh /usr/local/freesurfer/7.4.1/subjects single_subj /usr/local/freesurfer/7.4.1/subjects/workbench_freesurfer

Output & Error
--------------------
START: FS2CaretConvertRegisterNonlinear
Saving /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.white.native.surf.gii as a surface in TKREGISTER space
Saving /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.pial.native.surf.gii as a surface in TKREGISTER space
Saving /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.sphere.reg.native.surf.gii as a surface in TKREGISTER space
Saving /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.sphere.native.surf.gii as a surface in TKREGISTER space

While running:
wb_command -set-structure /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.sulc.native.shape.gii CORTEX_LEFT

ERROR: NAME OF FILE: single_subj.L.sulc.native.shape.gii
PATH TO FILE: /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench

File does not exist.

Thanks,
Michael
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20250515/cf700455/attachment.htm>