Yes, the output is in native functional space. On 7 November 2017 at 16:40, Douglas N Greve <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>> 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:freesur...@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 >
_______________________________________________ Freesurfer mailing list 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 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.
