you probably can't use label files as input to probtraxx. Instead, you
should convert the aparc+aseg.mgz file to the native diffusion space.
First register the low b to the freesurfer anatomical using bbregister
(and check with tkregister2). Then use mri_label2vol to convert the
aparc+aseg.mgz to the native diffusion space (store as nifti). Then
extract a binary volume from the aparc+aseg.nii for the label you want.
You can do this with mri_binarize. Use the --match option with something
like 1001 for lh bankssts (see $FREESURFER_HOME/FreeSurferColotLUT.txt
for the table of numbers and structures).

doug

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__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
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.