Dear a.y.

Thanks for getting back.

I’ve set the wheels in motion to run tracula on the control scans that we have.

I found your notes in the diffusion_tutorial download for grabbing the bval and bvecs from each DTI slice which looks like the biggest difficulty.

On most of our controls, we have scans at several b-values, 1000, 3000, 5000, 7000.

Is there a way to use all 4?

And even if there is, which would be the best single one to use?

Best – Don

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, February 14, 2018 6:22 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI

That's correct, you'd have to run TRACULA on a subject to get those files. They're computed from those 33 subjects, but you can't get the info without running it unfortunately.

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Krieger, Donald N. <kriegerd@upmc.edu>
Sent: Wednesday, February 14, 2018 5:19:48 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI

Thank you very much for getting back on this so promptly, a.y.

If I understand correctly, I think it’s the information in the *_fsids_all_0_0_0.txt files from tracula runs on your training subjects, trc001-trc033, that would be best to use.

I see the trctrain directory with its contents in my Freesurfer 5.3 installation and presume that this is all that’s here. Are those .txt files readily available somewhere? Or do I need to do my own tracula runs to get them?

Or am I missing something?

I am a total newbie on tracula.

Best – Don

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, February 14, 2018 4:34 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI

Hi Donald – TRACULA doesn’t use deterministic ROIs, instead it assigns a probability to any ROI to be the one that the specific tract intersects or neighbors at a specific position along that tract’s trajectory. These prior probabilities are computed from the training subjects that make up the TRACULA atlas (where atlas here refers to a set of individuals rather than an average brain).

For what you’re looking for, find the files: $yoursubject/dlabel/mni/*_fsids_all_0_0_0.txt

There is one file for each tract. The 0_0_0 in the file name means that you’re looking at the ROIs that tract goes through (rather than the tract’s left, right, etc neighbors - there are other files for those). In each of these files, each line corresponds to a different position along the tract. Since you’re interested in the endpoints, you want to look at the first and the last line. The ID numbers in that file correspond to ROIs as specified in $FREESURFER_HOME/FreeSurferColorLUT.txt.

Hope this helps,

a.y

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Krieger, Donald N." <kriegerd@upmc.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, February 14, 2018 at 10:19 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] List needed: pathway <==> freesurfer ROI

Dear List,

I need a list of Freesurfer ROIs which are typical endpoints for each standard pathway used in tracula.

I think this information is likely included in the default tracula atlas which I have been unable to find although I do not need spatial coordinates but rather just the list of ROI names for each pathway.

If this information is contained in publications, I would like to cite them.

I hope this is clear and thank you for any help you can provide.

Best - Don

Don Krieger, Ph.D.

Research Scientist

Department of Neurological Surgery

University of Pittsburgh