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
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
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 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 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
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.
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> > 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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 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 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
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.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
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> > 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. 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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>
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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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looks like you did not create the lta file properly. You can just pass mris_preproc the .dat file instead of the lta.
On 11/07/2017 10:51 AM, Elisa Castaldi wrote:
Yes, the output is in native functional space.
On 7 November 2017 at 16:40, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto: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> > <mailto: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> <mailto: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> >> <mailto: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> >> <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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> >> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://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> >> <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> >> <http://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/> >> <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> >> <mailto: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> >> <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> >> <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> >> <mailto: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> >> <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> <mailto: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> > <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> > <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> -- 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>
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Thank you very much for your help, that almost fixed the problem.. Indeed it seems like it worked well for the first subject, but then it crashed for the second one.. this is the last part of what it typed on the command window:
%%%%%%%%%%%%%%%%%%%%% Cleaning up ----------------------- rm -r ./tmp.mris_preproc.2277 mardi 7 novembre 2017, 17:12:21 (UTC+0100) mris_preproc done SUBJECTS_DIR$ --iv ${SUBJECTS_DIR}/sub02/stats/con_0001.nii ${SUBJECTS_DIR}/sub02/fmri/bbrumeanSBref_sess1_mb1.dat\
--projfrac 0.5 \
--iv : commande introuvable
For the first subject it correctly created the lh.con.mris_preproc.log file Any idea? Thanks
On 7 November 2017 at 17:00, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
looks like you did not create the lta file properly. You can just pass mris_preproc the .dat file instead of the lta.
On 11/07/2017 10:51 AM, Elisa Castaldi wrote:
Yes, the output is in native functional space.
On 7 November 2017 at 16:40, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto: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 andthe
> 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> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > When you look in SUBJECTS_DIR, you should see fsaverage andall
> 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> <mailto: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> >> <mailto: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> >> <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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> >> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://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> >> <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> >> <http://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/> >> <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> >> <mailto: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> >> <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> >> <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> >> <mailto: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> >> <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> <mailto: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> > <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> > <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> -- 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>
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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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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It looks like it is a scripting problem where you did not include a backslash to indicate that the command line continued to the next line and so it thinks that "-=-iv" is a command (I assume that "commande introuvable" means something like "command not found")
On 11/9/17 12:39 PM, Elisa Castaldi wrote:
Thank you very much for your help, that almost fixed the problem.. Indeed it seems like it worked well for the first subject, but then it crashed for the second one.. this is the last part of what it typed on the command window:
%%%%%%%%%%%%%%%%%%%%% Cleaning up
rm -r ./tmp.mris_preproc.2277 mardi 7 novembre 2017, 17:12:21 (UTC+0100) mris_preproc done SUBJECTS_DIR$ --iv ${SUBJECTS_DIR}/sub02/stats/con_0001.nii ${SUBJECTS_DIR}/sub02/fmri/bbrumeanSBref_sess1_mb1.dat\
--projfrac 0.5 \
--iv : commande introuvable
For the first subject it correctly created the lh.con.mris_preproc.log file Any idea? Thanks
On 7 November 2017 at 17:00, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
looks like you did not create the lta file properly. You can just pass mris_preproc the .dat file instead of the lta. On 11/07/2017 10:51 AM, Elisa Castaldi wrote: > Yes, the output is in native functional space. > > On 7 November 2017 at 16:40, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto: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> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto: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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > >> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > >> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > >> > >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > >> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <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> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > >> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://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/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > >> <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <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> > <mailto: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> > <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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <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> > <http://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/> > <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> <mailto: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> > <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> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 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>
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Thank you very much, now it is working! The backslash was there but there was no space just after the .dat I report below the final commands that I have used in case somebody else might find it useful. Thanks again!
mris_preproc --target fsaverage --hemi lh \ --iv ${SUBJECTS_DIR}/sub01/stats/con_0001.nii ${SUBJECTS_DIR}/sub01/fmri/bbrumeanSBref_sess1_mp1.dat \ --iv ${SUBJECTS_DIR}/sub02/stats/con_0001.nii ${SUBJECTS_DIR}/sub02/fmri/bbrumeanSBref_sess1_mb1.dat \ --projfrac 0.5 \ --out lh.ces.mgh
On 10 November 2017 at 20:30, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
It looks like it is a scripting problem where you did not include a backslash to indicate that the command line continued to the next line and so it thinks that "-=-iv" is a command (I assume that "commande introuvable" means something like "command not found")
On 11/9/17 12:39 PM, Elisa Castaldi wrote:
Thank you very much for your help, that almost fixed the problem.. Indeed it seems like it worked well for the first subject, but then it crashed for the second one.. this is the last part of what it typed on the command window:
%%%%%%%%%%%%%%%%%%%%% Cleaning up
rm -r ./tmp.mris_preproc.2277 mardi 7 novembre 2017, 17:12:21 (UTC+0100) mris_preproc done SUBJECTS_DIR$ --iv ${SUBJECTS_DIR}/sub02/stats/con_0001.nii ${SUBJECTS_DIR}/sub02/fmri/bbrumeanSBref_sess1_mb1.dat\
--projfrac 0.5 \
--iv : commande introuvable
For the first subject it correctly created the lh.con.mris_preproc.log file Any idea? Thanks
On 7 November 2017 at 17:00, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
looks like you did not create the lta file properly. You can just pass mris_preproc the .dat file instead of the lta.
On 11/07/2017 10:51 AM, Elisa Castaldi wrote:
Yes, the output is in native functional space.
On 7 November 2017 at 16:40, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto: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 andthe
> 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> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > When you look in SUBJECTS_DIR, you should see fsaverage andall
> 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 itcannot
>> 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 givesthe
>> 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 zkaufmanExp $
>> 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> <mailto: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 outputfile
>> (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 folderper
>> 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> >> <mailto: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> >> <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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> >> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://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> >> <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> >> <http://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/> >> <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> >> <mailto: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> >> <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> >> <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> >> <mailto: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> >> <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> <mailto: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> > <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> > <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> -- 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>
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 <(617)%20724-2358> Fax: 617-726-7422 <(617)%20726-7422>
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 listFreesurfer@nmr.mgh.harvard.eduhttps://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.
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Elisa Castaldi