Hi Patrica,
recently I asked the question about surface tracking on the FSL mailing list and got an answer that you can track FROM the surface, but not TO surface, in other words you can not use FS label as a waypoint. The way to go is as Dough suggest in his followup.
Best,
Martin
On Thursday 17 June 2010 22:40:13 oxro0@yahoo.com wrote:
Hi,
I am trying to use Freesurfer parcellations as seed-, way- and endpoints for FSL's ProbtrackX and am following the suggestions here: http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html
I was able to specify surface labels as seed points, but get error messages when trying to do the same with end- and waypoints:
Below is the command line and the error. Any suggestions on how to do this with FS parcellations would be much appreciated!
Thanks,
Patricia
/usr/pubsw/packages/fsl/fsl-4.0.4_RH4_64/bin/probtrackx --seedref=/space/emc2/1/halgdev/projects/NYU/morphometry/DTI/NY248_fmri__ni i_032510/09+cbi_ep2d_diff_b1000/test6/dti_struct_brain.nii.gz -o /space/emc2/1/halgdev/projects/NYU/morphometry/DTI/NY248_fmri__nii_032510/ 09+cbi_ep2d_diff_b1000/test10/test10 -x $SUBJECTS_DIR/NY248_fmri_032510/label/lh.rostralanteriorcingulate.label --mesh=$SUBJECTS_DIR/NY248_fmri_032510/surf/lh.white.asc -l -c 0.2 -S 2000 --steplength=0.5 -P 1000 --xfm=/space/emc2/1/halgdev/projects/NYU/morphometry/DTI/NY248_fmri__nii_03 2510/09+cbi_ep2d_diff_b1000/test6/dti_struct2fa.mat --forcedir --opd -s /space/emc2/1/halgdev/projects/NYU/morphometry/DTI/NY248_fmri__nii_032510/0 9+cbi_ep2d_diff_b1000/fdt.bedpostX/merged -m /space/emc2/1/halgdev/projects/NYU/morphometry/DTI/NY248_fmri__nii_032510/0 9+cbi_ep2d_diff_b1000/fdt.bedpostX/nodif_brain_mask --dir=/space/emc2/1/halgdev/projects/NYU/morphometry/DTI/NY248_fmri__nii_0 32510/09+cbi_ep2d_diff_b1000/test10/ --stop=$SUBJECTS_DIR/NY248_fmri_032510/label/lh.bankssts.label
Log directory is: /space/emc2/1/halgdev/projects/NYU/morphometry/DTI/NY248_fmri__nii_032510/0 9+cbi_ep2d_diff_b1000/test10/
** ERROR (nifti_image_read): failed to find header file for '/home/halgdev/projects/nyuproj/subjects//NY248_fmri_032510/label/lh.bankss ts.label'
** ERROR: nifti_image_open(/home/halgdev/projects/nyuproj/subjects//NY248_fmri_032510 /label/lh.bankssts.label): bad header info
Error: failed to open file /home/halgdev/projects/nyuproj/subjects//NY248_fmri_032510/label/lh.bankss ts.label
ERROR: Could not open image /home/halgdev/projects/nyuproj/subjects//NY248_fmri_032510/label/lh.banksst s.label
Image Exception : #22 :: Failed to read volume /home/halgdev/projects/nyuproj/subjects//NY248_fmri_032510/label/lh.banksst s.label
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Read otherAbort