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 the registration
>>
>> 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, 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>
>> >
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>> <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>
>>
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>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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>> <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/>
>>
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--
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
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