On 7 November 2017 at 17:00, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

looks like you did not create the lta file properly. You can just pass
mris_preproc the .dat file instead of the lta.

On 11/07/2017 10:51 AM, Elisa Castaldi wrote:
> Yes, the output is in native functional space.
>
> On 7 November 2017 at 16:40, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> Did you keep the spm output in native functional space?
>
>
> On 11/07/2017 09:23 AM, Elisa Castaldi wrote:
> > Yes,
> > this is what I have already done: I moved both the fsaverage and the
> > subjects into SUBJECTS_DIR and the error I get is ERROR: source
> volume
> > is neither source nor target of the registration.
> >
> > On 7 November 2017 at 15:11, Douglas Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu

> <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> >
> > 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
> >> <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>

> <mailto:greve@nmr.mgh.harvard.edu

> <mailto: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
> <mailto:Freesurfer@nmr.mgh.harvard.edu>

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> >>
> >> --
> >> Douglas N. Greve, Ph.D.
> >> MGH-NMR Center
> >> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 <tel:617-724-2358>
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--
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MGH-NMR Center
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