Dear Freesurfer users,
I would like to perform surface based fMRI gorup analysis in Freesurfer
starting from SPM first level output files, but I am not succeding.
I have already preprocessed the data in spm and used Freesurfer for
boundary based registration, I have succesfully ran the recon -all comand
and ovelayed the first level analysis output file (created with spm).
Now I would like to perform surface based fMRI group analysis with
Freesurfer, but I am worried it is crashing either because the folders are
not organized the way they should or because I am missing some files.
first I have converted .dat into .lta file
tkregister --mov bbrumeanSBref_sess1_mp1.nii --targ
bbrumeanSBref_sess1_mp1.nii --reg bbrumeanSBref_sess1_mp1.dat --ltaout
mp1reg.lta --noedi
then
mris_preproc --out lh.con.mgh --target ${SUBJECTS_DIR}/surfaces/fsaverage
--hemi lh \
--iv ${SUBJECTS_DIR}/sub01/stats/con_0001.nii
${SUBJECTS_DIR}/sub01/fmri/mp1reg.lta\
--iv ${SUBJECTS_DIR}/sub02/stats/con_0001.nii
${SUBJECTS_DIR}/sub02/fmri/ab1reg.lta\
--projfrac 0.5 \
ERROR: cannot find SUBJECTS_DIR/surfaces/fsaverage in SUBJECTS_DIR
Trying to move files in the requested directory caused other errors,
everytime not finding what it needs.
At the moment the project folder contains one folder per each subject (each
one containing fmri, stats, t1mri folders, containing spm results) and one
folder called 'surfaces' containing 1) the fs average and 2)one folder per
subject containing the results of the recon -all command.
Is it possible to run the surface based group analysis if I have not used
Freesurfer since the beginning? How should I reorganize the directories?
I could not find any related issue in the archive.
Thanks a lot for your help
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