[FieldTrip] Help Running ft_postfreesurferscript.sh

[Michael Houston]

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://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Fsource%2Fsourcemodel%2F&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C95dfd5f11eba45cd573208dd8e357ca4%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638823082693275361%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C60000%7C%7C%7C&sdata=wUJlkWjQA02TxUNt1x89ngMWIqezHUHZWoafJdc51Ts%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
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