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If all you want is FA, you don’t have to run bedpostx, just dtifit. For HCP data, you would want to use -g flag too for bedpostx if you are running it. For use of CUDA, you need to make sure you have a CUDA capable GPU and all the CUDA dependencies installed.
You might get better help with that on the FSL mailing list, though perhaps those folks will respond here too.
Peace,
Matt.
From: <Chiu>, "Bryan (PHTH)" <[email protected]>
Date: Thursday, May 7, 2015 at 2:57 PM To: "[email protected]" <[email protected]> Subject: [HCP-Users] HCP Anatomical FA values. Hi,
I have a few questions that I hope someone can outline for me. My goal at the moment is to extract FA values for anatomical regions in the brain within the HCP participants.
I was attempting to closely follow the pipeline outlined in this link (http://polaris.ssc.uwo.ca/mediawiki/index.php/DTI_analysis) with some changes to allow for the use of CUDA.
at the current moment I am trying to run bedpostx on a single participant but it is crashing immediately:
>bedpostx_gpu Diffusion -n 3 --cnonlinear --rician --model=3
It crashes in both the stripped down version of the command (bedpostx <Directory> and the one that I have tried above.
here is the error log:
"
terminate called after throwing an instance of 'NEWMAT::IndexException' /bin/sh: line 1: 4602 Aborted (core dumped) /usr/local/fsl/bin/xfibres_gpu --data="" --mask=/home/TLA/Desktop/100307/T1w/Diffusion.bedpostX/nodif_brain_mask -b /home/TLA/Desktop/100307/T1w/Diffusion.bedpostX/bvals -r /home/TLA/Desktop/100307/T1w/Diffusion.bedpostX/bvecs --forcedir --logdir=/home/TLA/Desktop/100307/T1w/Diffusion.bedpostX/diff_parts/data_part_0000 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear /home/TLA/Desktop/100307/T1w/Diffusion 0 1 > /home/TLA/Desktop/100307/T1w/Diffusion.bedpostX/logs/log0000 "
I ran my FSL through FEEDS so I don't think it is an issue with my install of FSL or CUDA. I also did a brief check of the FSL and HCP mailing lists, but nothing had turned up. I wanted to see if theres some particularities with the data that are making this hard for me.
I would also like some feedback as to the pipeline I am using.
Many thanks in advance, ______________________________
Bryan Chiu Undergraduate Research Assistant Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy
Faculty of Medicine University of British Columbia _______________________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ |
- [HCP-Users] HCP Anatomical FA values. Chiu, Bryan (PHTH)
- Re: [HCP-Users] HCP Anatomical FA values. Glasser, Matthew
