Thanks a lot for the explanation and for offering the "hidden flag", Saad. I'll
keep it in mind and get back if I realize I could use it.
Cheers,
Martin
On Wednesday 09 June 2010 12:52:18 you wrote:
> Hi Martin,
> The surface tracking only allows you to track FROM the surface, and not TO
> a surface. If you want your tracts to stop at the frontal pole, you need
> to transform your label file into a volume file (e.g. using mri_label2vol)
> and feed it to probtrackx as waypoint and/or stopping mask. Note: you can
> also track from the hippocampus surface using FIRST segmentation, although
> this requires to use a hidden flag - let me know if you want to use this
> option.
>
> Cheers,
> Saad.
>
> On 9 Jun 2010, at 12:31, Martin Kavec wrote:
> > Hi,
> >
> > I am trying to do a surface tracking (using FreeSurfer surfaces) as
> > described on the FDT webpage
> > (http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html), but I am not sure
> > if I do it right. I have generated and verified the
> > transformations, which seem to work. The problem I have is with the
> > probtrackx command arguments.
> >
> > I would like to seed from a small volume in the hippocampus (defined as
> > nii.gz) and track to a surface (defined as label). Here is the command I
> > used and which results only to the hippocampal ROI:
> >
> > probtrackx -x hippocamp_roi.nii.gz --mesh=../surf/lh.white.asc -l -c 0.2
> > -S 2000 --steplength=0.5 -P 5000 --forcedir --opd -s
> > data.bedpostX/merged -m data/nodif_brain_mask.nii.gz
> > --dir=data.probtrackx --
> > xfm=anat/FS_2_FA_fnirt.nii.gz --invxfm=anat/FA_2_FS_fnirt.nii.gz --
> > seedref=anat/brainmask.nii.gz --mesh=../label/lh.frontalpole.label
> >
> > Thanks for advice in advance,
> >
> > Martin
>
> --
> Saad Jbabdi
> University of Oxford, FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> (+44)1865-222466 (fax 717)
> www.fmrib.ox.ac.uk/~saad
--
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Senior Clinical Research Associate in Neuroradiology
MRI Unit of the Department of Radiology
Erasme Hospital
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