Thanks for your answer. If I don't specify the directory I get the following error ERROR: cannot find fsaverage in SUBJECTS_DIR
and if I move fsaverage to SUBJECTS_DIR it says that it cannot find manat_mp1 which is the name of the folder containing the results of recon all for the subject sub01 (contained in the SUBJECTS_DIR/surfaces folder). If then I move the manat_mp1 folder into SUBJECTS_DIR it starts running, but then gives the following error ERROR: source volume is neither source nor target of the registration. Below the entire list of output printed before the error
mris_preproc --out lh.con.mgh --target fsaverage --hemi lh \
--iv ${SUBJECTS_DIR}/sub01/stats/con_0001.nii
${SUBJECTS_DIR}/sub01/fmri/mp1reg.lta\ nsubjects = 1 tmpdir is ./tmp.mris_preproc.30824 SUBJECTS_DIR Log file is lh.con.mris_preproc.log
setenv SUBJECTS_DIR cd /SUBJECTS_DIR /i2bm/local/freesurfer/bin/mris_preproc --out lh.con.mgh --target fsaverage --hemi lh --iv /SUBJECTS_DIR/sub01/stats/con_0001.nii /SUBJECTS_DIR/sub01/fmri/mp1reg.lta
$Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.30824 Src lh sphere.reg Trg lh sphere.reg
--------------------------------------------------- #@# 1/1 manat_mp1 -------------- ----------------------- mri_vol2surf --src /SUBJECTS_DIR/sub01/stats/con_0001.nii --srcreg /SUBJECTS_DIR/sub01/fmri/mp1reg.lta --hemi lh --out ./tmp.mris_preproc.30824/subjsurfvals.mgh --cortex --noreshape srcvol = SUBJECTS_DIR/sub01/stats/con_0001.nii srcreg = /SUBJECTS_DIR/sub01/fmri/mp1reg.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Input reg is LTA
type = 0 # LINEAR_VOX_TO_VOX nxforms = 1 mean = 0.0000 0.0000 0.0000 sigma = 10000.0000 1 4 4 9.999966621398926e-01 2.551120938733220e-03 5.084594013169408e-04 -5.488281250000000e-01 4.461563366930932e-04 2.438484877347946e-02 -9.997024536132812e-01 2.180384216308594e+02 -2.562706125900149e-03 9.996992945671082e-01 2.438353188335896e-02 -5.147048950195312e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 src volume info valid = 1 # volume info valid filename = /SUBJECTS_DIR/sub01/fmri/bbrumeanSBref_sess1_mp1.nii volume = 256 256 256 voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00 xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00 zras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 cras = 1.867614746093750e+00 -1.400651550292969e+01 4.246002197265625e+00 dst volume info valid = 1 # volume info valid filename = /SUBJECTS_DIR/sub01/fmri/bbrumeanSBref_sess1_mp1.nii volume = 256 256 256 voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00 xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00 zras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 cras = 1.867614746093750e+00 -1.400651550292969e+01 4.246002197265625e+00 subject manat_mp1 fscale 0.150000
ERROR: source volume is neither source nor target of the registration
Any other suggestions? Thanks a lot
On 6 November 2017 at 23:42, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
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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