Thank you very much for your help,
that almost fixed the problem.. Indeed it seems like it worked well for the
first subject, but then it crashed for the second one..
this is the last part of what it typed on the command window:
%%%%%%%%%%%%%%%%%%%%%
Cleaning up
-----------------------
rm -r ./tmp.mris_preproc.2277
mardi 7 novembre 2017, 17:12:21 (UTC+0100)
mris_preproc done
SUBJECTS_DIR$ --iv ${SUBJECTS_DIR}/sub02/stats/con_0001.nii
${SUBJECTS_DIR}/sub02/fmri/bbrumeanSBref_sess1_mb1.dat\
> --projfrac 0.5 \
>
--iv : commande introuvable
For the first subject it correctly created the lh.con.mris_preproc.log file
Any idea?
Thanks
On 7 November 2017 at 17:00, Douglas N Greve <gr...@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
> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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
> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> > > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@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
> > >> <gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto: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
> > >> >
> > >> >
> > >> >
> > >> > _______________________________________________
> > >> > Freesurfer mailing list
> > >> > Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >> >
> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/
> freesurfer
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >>
> > >> --
> > >> Douglas N. Greve, Ph.D.
> > >> MGH-NMR Center
> > >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu
> >>
> > >> Phone Number: 617-724-2358 <tel:617-724-2358>
> > <tel:617-724-2358 <tel:617-724-2358>>
> > >> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
> > <tel:617-726-7422>>
> > >>
> > >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > >> <https://gate.nmr.mgh.harvard.edu/filedrop2
> > <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > >>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > >> Outgoing:
> > >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> > >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/
> flat/greve/
> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> > >>
> > >> _______________________________________________
> > >> Freesurfer mailing list
> > >> Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/
> freesurfer
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >>
> > >>
> > >> The information in this e-mail is intended only for the
> > >> person to whom it is
> > >> addressed. If you believe this e-mail was sent to you in
> > >> error and the e-mail
> > >> contains patient information, please contact the Partners
> > >> Compliance HelpLine at
> > >> http://www.partners.org/complianceline
> > <http://www.partners.org/complianceline>
> > >> <http://www.partners.org/complianceline
> > <http://www.partners.org/complianceline>> . If the e-mail was
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> > >>
> > >> _______________________________________________
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> > >
> > >
> > > _______________________________________________
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> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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> > >
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> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> > >
> > > The information in this e-mail is intended only for the
> > person to
> > > whom it is
> > > addressed. If you believe this e-mail was sent to you in
> > error and
> > > the e-mail
> > > contains patient information, please contact the Partners
> > > Compliance HelpLine at
> > > http://www.partners.org/complianceline
> > <http://www.partners.org/complianceline>
> > > <http://www.partners.org/complianceline
> > <http://www.partners.org/complianceline>> . If the e-mail was sent
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> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> > Phone Number: 617-724-2358 <tel:617-724-2358>
> > Fax: 617-726-7422 <tel:617-726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.
> harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> >
> >
> >
> > _______________________________________________
> > 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/
>
> _______________________________________________
> Freesurfer mailing list
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>
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