Dear FreeSurfer users,
I am using Freesurfer 6.0 and Tracula 6.0 for processing MRI and DTI scans. The second step of the trac-all pipeline performs the ball-and-stick fit with the bedpost function from FSL. Documentation for FSL suggests that the use of GPUs can considerably speed this process (from ~15 hours on a single-threaded machine to 30 minutes on GPU; see bulletpoint 7 under processing pipeline at https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Processing_pipeline).
Using GPU requires calling "bedpostx_gpu" (instead of "bedpostx") on a machine with a NVIDIA GPU and CUDA toolkit, both of which I have access to. The "bedpostx_gpu" function has, otherwise, the same flags as "bedpostx".
While there is another post on the FreeSurfer forum on this topic (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg54498.html), the answer there does not refer to how "bedpostx_gpu" can be used.
Is there a way to call on "bedpostx_gpu" instead of "bedpostx" in the second step of the trac-all pipeline? More precisely, is there a way to adjust the command:
trac-all -bedp -c dmrirc
to take advantage of GPU capabilities?
Alternatively, is the source code for the "trac-all" binary available? For example, if is there a bash script that performs the same steps as the "trac-all -bedp -c dmrirc" available, then GPU capabilities can be exploited by running that script except replacing "bedpostx" with "bedpostx_gpu".
Thank you.
Best,
Chintan