Re: [Freesurfer] cortical parcellations & ProbtrackX

Probably so. Just use the gray matter as seed points

oxro0@yahoo.com wrote:

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 </mc/compose?to=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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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu </mc/compose?to=greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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