| 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__nii_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_032510/09+cbi_ep2d_diff_b1000/test6/dti_struct2fa.mat
--forcedir --opd -s
/space/emc2/1/halgdev/projects/NYU/morphometry/DTI/NY248_fmri__nii_032510/09+cbi_ep2d_diff_b1000/fdt.bedpostX/merged
-m
/space/emc2/1/halgdev/projects/NYU/morphometry/DTI/NY248_fmri__nii_032510/09+cbi_ep2d_diff_b1000/fdt.bedpostX/nodif_brain_mask
--dir=/space/emc2/1/halgdev/projects/NYU/morphometry/DTI/NY248_fmri__nii_032510/09+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_032510/09+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.bankssts.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.bankssts.label ERROR: Could not open image /home/halgdev/projects/nyuproj/subjects//NY248_fmri_032510/label/lh.bankssts.label Image Exception : #22 :: Failed to read volume /home/halgdev/projects/nyuproj/subjects//NY248_fmri_032510/label/lh.bankssts.label terminate called after throwing an instance of 'RBD_COMMON::BaseException' Read otherAbort |