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>
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>
> 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
>> > 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/
>>
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