Hi
The easiest way to test the transformation is to apply it to a freesurfer-conformed brain.
E.g.:
mri_convert $SUBJECTS_DIR/john/mri/brain.mgz $SUBJECTS_DIR/john/mri/brain.nii.gz
flirt -in $SUBJECTS_DIR/john/mri/brain.nii.gz \
-out test_struct2fa.nii.gz \
-ref dti_FA \
-applyxfm -init freesurfer2fa.mat
If this looks good, then the labels will end up in the right place in diffusion space.
Cheers,
Saad.
On 7 Mar 2011, at 10:31, Righart, Ruthger Dr. wrote:
> Dear All,
>
> In probtrackx it is possible to use a seed from a freesurfer cortical label, as shown at http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html.
>
> Under step 1 it is explained how to bring the label from freesurfer to diffusion space. At the end of step 1, one has a freesurfer2fa.mat file that is used in probtrackx, under step 3. But I was wondering whether it is possible to test if this transformation .mat file to diffusion space is correct, just to know that nothing went wrong along the way until here? Is it for example possible to view with fslview the original freesurfer label file in diffusion space, incorporating the transformation matrix freesurfer2fa.mat, to see whether the cortical label is really placed at the right position? I tried using the --xfm freesurfer2fa.mat command but this seems not possible in fslview.
>
> Thank you very much in advance for your help!
>
> Ruthger Righart (PhD)
> Institute for Stroke and Dementia Research (ISD)
> Klinikum der Universität München
> Max-Lebsche-Platz 30
> 81377 Munich | Germany
>
> [log in to unmask]
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
