Thank you very much, now it is working!
The backslash was there but there was no space just after the .dat
I report below the final commands that I have used in case somebody else
might find it useful.
Thanks again!
mris_preproc --target fsaverage --hemi lh \
--iv ${SUBJECTS_DIR}/sub01/stats/con_0001.nii
${SUBJECTS_DIR}/sub01/fmri/bbrumeanSBref_sess1_mp1.dat \
--iv ${SUBJECTS_DIR}/sub02/stats/con_0001.nii
${SUBJECTS_DIR}/sub02/fmri/bbrumeanSBref_sess1_mb1.dat \
--projfrac 0.5 \
--out lh.ces.mgh
On 10 November 2017 at 20:30, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> It looks like it is a scripting problem where you did not include a
> backslash to indicate that the command line continued to the next line and
> so it thinks that "-=-iv" is a command (I assume that "commande
> introuvable" means something like "command not found")
>
> On 11/9/17 12:39 PM, Elisa Castaldi wrote:
>
> Thank you very much for your help,
> that almost fixed the problem.. Indeed it seems like it worked well for
> the first subject, but then it crashed for the second one..
> this is the last part of what it typed on the command window:
>
> %%%%%%%%%%%%%%%%%%%%%
> Cleaning up
> -----------------------
> rm -r ./tmp.mris_preproc.2277
> mardi 7 novembre 2017, 17:12:21 (UTC+0100)
> mris_preproc done
> SUBJECTS_DIR$ --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/bbrum
>> eanSBref_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/bbrum
>> eanSBref_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
>> > >> sent to you in error
>> > >> but does not contain patient information, please
>> > contact the
>> > >> sender and properly
>> > >> dispose of the e-mail.
>> > >>
>> > >>
>> > >>
>> > >>
>> > >> _______________________________________________
>> > >> 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/freesurf
>> er
>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
>> > >
>> > >
>> > > _______________________________________________
>> > > 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 sent
>> > > to you in error
>> > > but does not contain patient information, please contact the
>> > > sender and properly
>> > > dispose of the e-mail.
>> > >
>> > >
>> > >
>> > >
>> > > _______________________________________________
>> > > 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.har
>> vard.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 <(617)%20724-2358>
>> Fax: 617-726-7422 <(617)%20726-7422>
>>
>> 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
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>
>
>
> _______________________________________________
> Freesurfer mailing
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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> Freesurfer@nmr.mgh.harvard.edu
> 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
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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