thank you. I'll try that.
might it be better to use the white matter parcellations (wmparc.mgz) as tractography way points and end points instead of gray matter parcellations (aseg)?
Thanks!
--- On Thu, 6/17/10, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cortical parcellations & ProbtrackX To: "oxro0@yahoo.com" oxro03@yahoo.com Cc: behrens@fmrib.ox.ac.uk, freesurfer@nmr.mgh.harvard.edu Date: Thursday, June 17, 2010, 1:50 PM
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
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