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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