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>> 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>> 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> >> > >> 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:Freesurfer@nmr.mgh.harvard.edu> >> 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> . 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> > > > _______________________________________________ > 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> > > > 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> . 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 > 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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
