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Hi Michael,
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<div>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?)</div>
<div>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).</div>
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<div>Best wishes,</div>
<div>Jan-Mathijs</div>
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<div>On 8 May 2025, at 15:37, Michael Houston via fieldtrip <fieldtrip@science.ru.nl> wrote:</div>
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<div>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 (<a href="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" originalsrc="https://www.fieldtriptoolbox.org/tutorial/source/sourcemodel/" originalsrc="https://www.fieldtriptoolbox.org/tutorial/source/sourcemodel/">https://www.fieldtriptoolbox.org/tutorial/source/sourcemodel/</a>)
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.</div>
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<div>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.:</div>
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<div>Command</div>
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<div>/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</div>
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<div>Output & Error</div>
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<div>START: FS2CaretConvertRegisterNonlinear<br>
Saving /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.white.native.surf.gii as a surface in TKREGISTER space<br>
Saving /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.pial.native.surf.gii as a surface in TKREGISTER space<br>
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<br>
Saving /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.sphere.native.surf.gii as a surface in TKREGISTER space<br>
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While running:<br>
wb_command -set-structure /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.sulc.native.shape.gii CORTEX_LEFT<br>
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ERROR: NAME OF FILE: single_subj.L.sulc.native.shape.gii<br>
PATH TO FILE: /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench<br>
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File does not exist.</div>
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<font face="arial, sans-serif">Thanks,</font></div>
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<font face="arial, sans-serif">Michael</font></div>
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https://doi.org/10.1371/journal.pcbi.1002202<br>
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