7 Nov
2017
7 Nov
'17
10:51 a.m.
Yes, the output is in native functional space.
On 7 November 2017 at 16:40, Douglas N Greve 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> 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 theregistration
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>>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, containingspm
> 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 greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@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