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There is no way to do this. All the fsfast commands are going to expect things to be in the fsfast directory structure.

On 8/11/2023 12:19 PM, Noah Lee wrote:

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Hello!

I am trying to run some freesurfer commands for a pipeline. However, I am coming in with functional data preprocessed by FEAT (EPI correction and general mcflirt, etc). For reference, I'm trying to run this following script:

preproc-sess -s . -fwhm 5 -stc siemens -surface fsaverage lhrh -per-run -fsd bold -mni305 -force
fcseed-config -wm -fcname wm.dat -fsd bold -mean -cfg wm.config -force
fcseed-config -vcsf -fcname vcsf.dat -fsd bold -mean -cfg vcsf.config -force
fcseed-sess -s . -cfg wm.config -force
fcseed-sess -s . -cfg vcsf.config -force

I am obviously skipping the preproc-sess step, as my data has been preprocessed. However, I'm not too sure how to run the following steps with the outputs of my feat directory. If anyone could help, I would greatly appreciate it!

Best,

Noah Lee
he/him/his
Yale University | Saybrook '25
B.S. Neuroscience


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