Hi Martijn - You could check how the ILF of the atlas subjects aligns with your subject's anatomical segmentation. These files are all in MNI space here: dlabel/mni/aparc+aseg.nii.gz dlabel/mni/aparc+aseg_mask.nii.gz (dilated version used as a brain mask) dlabel/mni/lh.ilf_*_histo.nii.gz

Note that any ILF streamlines from the atlas that go off the brain mask of your subject have been removed before creating the *histo.nii.gz file, so you can compare with a healthy subject and see if there's much less left in the pathological subject, and if what's there goes through the same parts of the aparc+aseg in both cases.

Hope this helps, a.y

On Thu, 1 Mar 2012, Martijn Steenwijk wrote:

Thanks for your reply, sorry for the delay. The problems appear in the left hemisphere ILF_AS. The subject has atrophy and a number of periventricular lesions.  Does the error indicate that set of the endpoints could not be mached? In that case it could be that the points in the temporal pole give problems since the original FS segmentation is a bit too tight there. Is there a way to visualize the suspected points onto the subjects data?

Best, Martijn

On Mon, Feb 27, 2012 at 10:16 PM, ayendiki@nmr.mgh.harvard.edu wrote: Hi Martijn,

  Which pathway does it fail on? Is the pathology of your subject
  affecting
  the structures in the aparc+aseg that surround that pathway?

  a.y

...

Dear all,

I'm running Tracula on a brain with some pathology. During the

preproc

...

phase it fails with the following error:

INFO: Rejected 843 streamlines for straying off mask INFO: Rejected 0 streamlines for reversing direction INFO: Rejected 10 streamlines as length outliers INFO: Have 2748 total streamlines (min/mean/max length: 38/70/105) Processing pathway 3 of 18... Matching streamline ends INFO: Have 0 non-truncated streamlines (min/mean/max length: 0/0/0) INFO: Center of mass of start points: (nan+/-nan, nan+/-nan,

nan+/-nan)

...

INFO: Center of mass of midpoints: (nan+/-nan, nan+/-nan, nan+/-nan) INFO: Center of mass of end points: (nan+/-nan, nan+/-nan,

nan+/-nan)

...

Segmentation fault (core dumped) Linux lnx-rad-03 2.6.18-92.1.18.el5 #1 SMP Wed Nov 5 09:00:19 EST

2008

...

x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Mon Feb 27 19:41:00 CET 2012

I understand that no streamlines are available for initialization.

Is that

...

correct?

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

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