When you look in SUBJECTS_DIR, you should see fsaverage and all the
subjects being passed to mris_preproc. If not, you need to move them (or
sym link them) into that folder.
On 11/7/17 6:07 AM, Elisa Castaldi wrote:
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 <mailto: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
>
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
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