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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> Freesurfer@nmr.mgh.harvard.edu
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422
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