Hello, Never mind. I was able to figure it out. I only needed to add "Users/Paul/Desktop" to the command line

On Wed, Aug 10, 2016 at 12:50 PM, miracle ozzoude miracooloz@gmail.com wrote:

Hello FreeSurfer experts, I am running surfaced based analysis using ROI approach. My mris_preproc, mri_surf2surf and mri_glmfit worked as expected. Since i restricted the region i built my own monte carlo "mri_mcsim --o roianalysis/average/mult-comp-cor/fsaverage/rh/rightmaskforcomp --base mc-z --surface fsaverage rh --nreps 10000 --label 2mask" which worked. However, when I wanted to run the mri_glmfit-sim using this command line " mri-glmfit-sim --glmdir rh.score.glmdir --cache-dir roianalysis/average/mult-comp-cor --cache-label rightmaskforcomp --cache 2 pos --cwpvalthresh 0.05 --2spaces" i got an error

"setenv SUBJECTS_DIR users/paul/desktop/roianalysis FREESURFER_HOME/ applications/freesurfer original mri_glmfit command line ............

DoSim = 0 UseCache = 1 dopoll = 1 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 17.292581 ERROR: cannot find roianalysis/average/mult-comp-cor/fsaverage/rh/ rightmaskforcomp/fwhm17/pos/th20/mc.z.csd"

I looked into roianalysis/........./fwhm17/pos/th20/mc.z.csd and it does exist. I saw a post like this on the forum but it wasn't answered. How can I direct it to my simulation on my subjectfolder (i.e., desktop/roianalysis/......)? Thanks Paul