Hi. I'm completely stuck without more input from freesurfer experts. The
email was about tracula. Could you confirm that you received my question
and that I sent everything you requested? Thanks much.
--
John Davis, PhD
Cell: (520) 907-9769
jda...@mrn.org
_
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
Just a quick follow-up question,
For FD/DVARS or other "censoring" criteria -- using -tpexclusion worked
great for surface based analysis with mkanalsysis and selxavg3. Is there a
way to do this for seed-to-seed analysis (fcseedcor)?
Thanks!
On Thu, Jan 25, 2018 at 4:00 PM, Douglas N Greve
wrote
Hi Donatas – All sounds fine. You can process single time points, and you can
process subsets of time points if the DWI data from one of them is unusable.
The T1 base template is only used as a reference space for longitudinal
TRACULA, so it shouldn’t make a huge difference if one additional tim
Hi John – The problem is the funky format of the numbers in that registration
file. It expects a 4x4 matrix of regular decimal numbers. Are the numbers in
all the other registration files in the xfms/ directory in this same format? It
probably has something to do with how your unix environment v
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 T
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 F
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.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Krieger, Donald N.
Sent:
