Hi Rohan,
On 06/30/14 11:37, Rohan Katipally wrote:
> Hi Martin,
> Your posts have been helpful, as I've been doing a similar analysis with freesurfer surface ROIs. So just to confirm with you, have you found that surface ROIs are giving you more robust results than when converting to volume ROIs (as described in http://sburns.org/2014/05/03/cortical-tractography-recipe.html), now that you've figured out the meshspace option?
I have not performed any quantitative analyses to confirm that the
results are more robust. It seems to me that using the mesh should in
theory be better given the way the targets/seeds are defined. I have
also found that some cross-hemispheric connections were absent when
using volumes.
Maybe one of the FSL developers can give more insight into the pros/cons.
> Furthermore, running probtrackx2 on all these surfaces (even when I run all my seeds in parallel on a cluster) take a long time. Have you tried decimating the surfaces (with mris_decimate) and have you found that it deteriorates results? I was planning on decimating to 1/2 or 1/3 of the original amount of vertices to speed up processing time. Because diffusion space is relatively low-res and tracking occurs in diffusion space, I can't imagine losing too much with even 1/3 of the original amount of vertices. I will probably confirm for myself, but just curious if you've tried it yourself.
Yes, it takes quite a long time and is very memory intensive. I have not
tried decimating the surfaces and I don't know if it is a good idea.
It would be great if probtrackx would use multiple threads to speed up
the estimation (so one could use e.g. 4 CPUs / 25GB memory on a cluster
node).
> Finally, if you don't mind me asking, what program did you use to make those visuals of the network? They look great.
The plots are done using MNE-Python and thanks (I wrote most of the
connectivity plot code):
http://martinos.org/mne/stable/mne-python.html
Best,
Martin
> Thanks,
> Rohan
>
>
>
--
Martin Luessi, Ph.D.
Research Fellow
Department of Radiology
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Harvard Medical School
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Charlestown, MA 02129
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