Hi there,

I am trying to run a Permutation Analysis of Linear Models (PALM) for analyzing 
subcortical areas in the nucleus accumbens, caudate, and putamen. Upon trying 
to run the script after reading the Freesurfer wiki, I am not sure what it is 
referring to regarding applying fsPalm in MATLAB. My questions are - do we a.) 
copy paste the existing fspalm command in Matlab and run it after setting the 
two Freesurfer paths listed in the wiki, or what is the correct procedure to 
run it? I tried running it in terminal as well, but didn’t have any luck. My 
existing Matlab script has set up the two Freesurfer paths, and is trying to 
run the fsPalm command for each subcortical area of the three ROIs mentioned 
above, but that isn’t working either. Any help in running fsPalm would be 
greatly appreciated!


Amritha Harikumar
Clinical Research Coordinator
Holt Emotion and Social Neuroscience Lab
Department of Psychiatric Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, Rm 2620A
Charlestown, MA 02129
Phone: 617-724-3283

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