Dear Freesurfers,

I want to run FSL probtrackx and use Freesurfer labels (aparc + asec) as seed and targets. I followed the instructions from here http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html to define the seed and the transformation.

However, I have problems defining Freesurfer labels as targets. These targets should be binary volume masks and they should be in the same space as the seed (hence, in the freesurfer conformed structural space). Now, I am not sure how to transform the labels into such binary masks.

As I see it, one option would be to take the aparc+aseg.mgz image and use mri_binarize to create such binary masks (one by one), e.g., mri_binarize --i aparc+aseg.mgz --o left_fusiform.nii.gz --match 1007

I am not confident that this is the correct way. In the Freesurfer mailing list, I read something that using mri_annotation2label and afterwards mri_label2vol is a better way. However, in that specific case from the mailing list the person also wanted the masks to be in native structural space – something I don’t need to have.

So basically, my question is whether the mri_binarize option is correct. Thanks a lot in advance (I know that there are several related threads in the mailing list archive – but nothing really answered my question).

Philipp

--- Philipp Ludersdorfer Department of Psychology and Center for Neurocognitive Research University of Salzburg Hellbrunner Strasse 34 5020 Salzburg