Anastasia-
This is super helpful! Thank you! I wrote a script to do exactly this and got something close (or exactly) to what I'm looking for, I think.
However, there are very few voxels in the voxelwise file--I traced them out and they're essentially the hottest voxels stored in path.pd.nii--it seems like I'm missing a large part of the probabalistic tract by doing this.
Maybe I'm a bit confused as to what exactly I'm doing.
-qf
Message: 8 Date: Thu, 27 Apr 2017 20:21:29 +0000 From: "Yendiki, Anastasia" AYENDIKI@mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA anterior/posterior {Disarmed} To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: AF49D39E2A7A3142903EC64E43DC0FAB889289ED@PHSX10MB10.partners.org Content-Type: text/plain; charset="windows-1252"
Hi Quentin - Yes, this is possible! You can use the info in the pathstats.byvoxel.txt files to do that. The -stat step of TRACULA (see last part of tutorial) will put together all the point-wise, along-the-tract stats of all the subjects into a table. Each element in the table will be one position along the tract for one subject. You can then average, say, the FA values from the first 1/3 of the positions and the last 1/3 of the positions, or something like that, to get the two endings of the tract that you care about.
Hope this helps, a.y ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Funk, Quentin [qfunk@houstonmethodist.org] Sent: Thursday, April 27, 2017 11:24 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] TRACULA anterior/posterior
Freesurfer experts:
I'm interested in comparing anterior and posterior pieces of a tract generated by TRACULA. Ideally, I'd like to take the probabilistic map (i.e. the path.pd.nii.gz from one of the folders in SUBJECT/dpath) and obtain a "posterior part" and an "anterior part" by masking. Then I'd like to extract stats similar to the stats found in pathstats.overall.txt
Is this at all possible? I can produce the poster/anterior mask by hand for each individual subject, (although if there were an automated way to do this that I'm unaware of it would be great) but getting the stats out is something I can't quite figure out from the tutorials I've looked through.
Thanks for any help!
Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003tel:713-363-9003
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