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 <gr...@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
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
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>
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