Hi Emily - Yes, this is fine. I just meant that it shouldn't look like a single line.

a.y

On Thu, 24 Jul 2014, ebelleau@uwm.edu wrote:

Hi Anastasia,

Just to be clear, is this what you mean by a more diffuse volumetric distribution. Here is a snapshot of the right inferior longitudinal fasiculous.

I am just getting a better sense of what to look for in terms of bad vs. good tracts.

Emily

----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 16, 2014 4:54:29 PM Subject: Re: [Freesurfer] Tracula : Path not entirely in the white matter

Hi Emily - This is not necessarily a problem. To make sure, you can check the output path.pd.nii.gz file from that specific tract. If it got stuck somewhere (e.g., because the brain mask is missing a bit of brain that this tract should go through) then the path.pd.nii.gz will look like a single curve rather than a more diffuse volumetric distribution.

Hope this helps, a.y

On Wed, 16 Jul 2014, ebelleau@uwm.edu wrote:

...

Hello,

I was looking at a trac-all log file to get my bearings on what is being done and making sure things were done successfully,

I did not get any errors for this subject but when I was looking at the right uncinate fasciculus: It would say "Path from initial control points not entirely in the white matter" and then it attempted to perturb control points.

I noticed that for this tract, it did not say that it did not say sucess after how ever many control points. It just said that it reverted back to the initial control points.

Do I then need to be concerned about the validity of this particular tract for this subject?

Thanks,

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

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