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muscbridge / PyDesigner

A hands-free DTI, DKI, FBI and FBWM preprocessing pipeline. Information on algorithms and preprocessing steps are available at https://www.biorxiv.org/content/10.1101/2021.10.20.465189v1 A video tutorial on PyDesigner and its usage is now available at https://www.youtube.com/watch?v=mChQFuQqX3k
https://pydesigner.readthedocs.io/en/latest/
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dwipreproc error with --undistort & --rpe_none options #101

Closed vadisetiyo closed 4 years ago

vadisetiyo commented 5 years ago

Describe the Issue Dataset: 2 DKI averages, 1 extra set of B0 averages Goal: Run PyDesigner with --undisort and --rpe_non options in order to register/align all my averages prior to DKI map calculation to improve map quality Issue: Unable to process dataset and get dwipreproc error (see attached jpg)

Issue Reproduction Dataset available in shared Box: All Files/PyDesigner_Testing/dwipreproc_Error/4042 Command ran: $ python /Users/adisetiyo/Desktop/PyDesigner/Software/PyDesigner/designer/pydesigner.py --denoise --undistort --smooth --rician --mask --rpe_none --verbose -o /Users/adisetiyo/Desktop/PyDesigner/4042/DKI_outputs /Users/adisetiyo/Desktop/PyDesigner/4042/DKI_inputs/4042_DIFF_siemens_dir_27_AVE1.nii,/Users/adisetiyo/Desktop/PyDesigner/4042/DKI_inputs/4042_DIFF_siemens_dir_27_AVE2.nii,/Users/adisetiyo/Desktop/PyDesigner/4042/DKI_inputs/4042_DKI_B0.nii

Supplemental Information OS: macOS Mojave Version 10.14.5 See attached snapshots for 1) Error; 2) System set up

10 28 19_dwipreprocError 10 28 19_PackageVersions
jbteves commented 5 years ago

Hi Vitria, this is I believe a known bug on OS X. You'll have to run it on a Linux docker environment. We should absolutely prioritize making a dockerfile and adding it to instructions. If you have a Linux partition you'll see it runs fine. Sorry, I think it totally slipped my mind to point this out in the meeting we had today. @TheJaeger do you have a dockerfile already to kickstart this?

TheJaeger commented 5 years ago

I'll invite you to collab on our dockerfile project. We can actually start kicking it off now that we have a somewhat working pipeline; dockerfiles stay somewhat the same once repos are defined.

TheJaeger commented 4 years ago

Issue was isolated to be an OS error. Refer to internal conversation below:

Screen Shot 2019-11-11 at 11 28 44 AM

The important information in this log is the third line from the bottom that says dwipreproc: [WARNING] CUDA version of eddy appears to have failed; trying OpenMP version. This warning implies that your machine doesn't support CUDA, so it runs the OpenMP version of eddy. This should be the correct behavior on non-CUDA devices like our Macs.