Hi again, To further clarify, I notice that in the tracula stream, there is an option to register to the cvs template. I assume that mri_vol2vol can accomplish the same thing, however. Is that correct? Also, do you know what files are required for mri_vol2vol? I can do this processing on our cluster, but I would rather not move all the files there! Best, Matt
-----Original Message----- From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] Sent: Thursday, June 06, 2013 11:48 AM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] averaging tracts?
Hi Matt - Thanks for your kind words!
The merged_*.mgz file is just a 4D mgz file where each frame corresponds to one of the 18 tracts. The only special thing about this mgz file is that it has some special fields in its header that tell freeview how to display each tract (color, name, and threshold). I haven't tried this, but I would guess that if you performed any operation on that mgz file, those header fields would be preserved. And if they're not they should be, so we should know about it.
You can try to map each mgz file from individual DWI space to a common space with mri_vol2vol and then average them with mri_concat. Let us know if this ends up working or if you have any questions about these steps.
Thanks! a.y
On Thu, 6 Jun 2013, Hoptman, Matthew wrote:
Hi all,
Thanks for tracula , which I think is a terrific tool. Is there any way to average tracts across subjects for viewing purposes? I have in mind somehting along the line of a group average merged_avg33_mni_bbi.mgz.
Thanks,
Matt
Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research
Research Associate Professor in Psychiatry NYU School of Medicine
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