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
>
>
>
> _______________________________________________
> 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
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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