Use
--target fsaverage
instead of giving the full path
On 11/06/2017 01:27 PM, Elisa Castaldi wrote:
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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