Thanks.
I'm using the documentation at http://fsl.fmrib.ox.ac.uk/fsl/fsl-4.1.9/fdt/fdt_surface.html.
Is it a correct way? For e.g. in the point 3 is indicated probtrackx -x .label ...
Now, in agreement with your indications, I'm correcting the command line.
The new's is reported below. Could you check it, please?
Please also note that thalami masks obtained form FreeSurfer (recon-all, mri_cor2label) are used as seed. Therefore, is I'm using label2surf -s <surface> -o <outputsurface> -l <labels>.
/usr/local/fsl/bin/probtrackx2
-s $SUBJECTS_DIR/DTI.bedpostX/merged
-m $SUBJECTS_DIR/DTI.bedpostX/nodif_brain_mask
-x $SUBJECTS_DIR/label/Right_Thalamus.gii
--meshspace=$SUBJECTS_DIR/surf/rh.white.nii.gz
--targetmasks=$SUBJECTS_DIR/mri/targets.txt
--dir=$SUBJECTS_DIR/HS
--forcedir
--opd
--os2t
--xfm=freesurfer2fa.mat
--seedref=$SUBJECTS_DIR/mri/nifti/brain
-l
--onewaycondition
-c 0.2
-S 2000
--steplength=0.5
-P 5000
--fibthresh=0.01
--distthresh=0.0
--sampvox=0.0
--convention=freesurfer
surf2surf -i <inputSurface> -o <outputSurface> [options] should be used?
I note that it is mentionated at http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide but not at http://fsl.fmrib.ox.ac.uk/fsl/fsl-4.1.9/fdt/fdt_surface.html
Stefano
Hi
I can see several problems:
1) you need to explicitly set surface convention: --convention=freesurfer
2) you can’t use a FreeSurfer label file as a seed. You need to use a GIFTI or ASCII surface file.
3) meshpace must be a NIFTI volume, not a surface file.
See the doc on how to do these things.
Saad
On 29 Apr 2014, at 08:05, Stefano <[log in to unmask]> wrote:
Hi list,
please help me to resolve this issue.
Thanks,
Stefano
/usr/local/fsl/bin/probtrackx2
-s $SUBJECTS_DIR/DTI.bedpostX/merged
-m $SUBJECTS_DIR/DTI.bedpostX/nodif_brain_mask
-x $SUBJECTS_DIR/label/Right_Thalamus.label
--meshspace=$SUBJECTS_DIR/surf/rh.white.asc
--targetmasks=$SUBJECTS_DIR/mri/targets.txt
--dir=$SUBJECTS_DIR/HS
--forcedir
--opd
--os2t
--xfm=freesurfer2fa.mat
--seedref=$SUBJECTS_DIR/mri/nifti/brain
--s2tastext
-l
--onewaycondition
-c 0.2
-S 2000
--steplength=0.5
-P 5000
--fibthresh=0.01
--distthresh=0.0
--sampvox=0.0
Running in seedmask mode
load seeds
CSV::set_convention: unknown convention $SUBJECTS_DIR/surf/rh.white.asc
Please note that I have already run.
mris_convert $SUBJECTS_DIR/surf/rh.white $SUBJECTS_DIR/surf/rh.white.asc
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
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