DKI Processing

[mmsarhan]

I just ran the command to process my DKI data and I was not sure if everything was processed as I received many error messages. I have pasted the full error list that came up on my terminal. Thank you
I just finished processing my files and this is what came up. I am not sure if everything ran correctly and wanted to ask. I have the full error messages that came up below. Thanks again for your help.

(DKE) [blab@localhost Scans]$ pydesigner -s DKI_BIPOLAR_2.5mm_64dir_50slices_20/
mrinfo: [done] scanning DICOM folder "/home/blab...LAR_2.5mm_64dir_50slices_20"
mrinfo: [100%] reading DICOM series "DKI_BIPOLAR_2.5mm_64dir_50slices"
mrconvert -quiet /home/blab/Downloads/Scans/dwi0.mif /home/blab/Downloads/Scans/working.mif
Insufficient information in .json file to determine Fourier status. Assuming DWI is partial Fourier
[WARNING] Given DWI is partial fourier, overriding --degibbs; no unringing correction will be done to avoid artifacts.Use the "--adv" flag to run forced corrections.
dwifslpreproc: [WARNING] DWI header indicates no phase encoding contrast between b=0 images; proceeding without inhomogeneity field estimation

dwifslpreproc: [ERROR] eddy* --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --repol --data_is_shelled --out=dwi_post_eddy --verbose (app.py:196)
dwifslpreproc: [ERROR] Information from failed command:
dwifslpreproc:
=============
eddy_cuda10.2
=============

           ===========
           eddy_openmp
           ===========
           
           
           =============
           eddy_cuda10.2
           =============
           eddy_cuda10.2: error while loading shared libraries: libcublas.so.10: cannot open shared object file: No such file or directory
           
           
           ===========
           eddy_openmp
           ===========
           eddy_openmp: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory

dwifslpreproc:
dwifslpreproc: [ERROR] For debugging, inspect contents of scratch directory: /home/blab/Downloads/Scans/dwifslpreproc-tmp-L7K02X/
Traceback (most recent call last):
File "/home/blab/anaconda3/envs/DKE/bin/pydesigner", line 8, in
sys.exit(main())
File "/home/blab/anaconda3/envs/DKE/lib/python3.7/site-packages/designer/pydesigner.py", line 644, in main
verbose=args.verbose)
File "/home/blab/anaconda3/envs/DKE/lib/python3.7/site-packages/designer/preprocessing/mrpreproc.py", line 481, in undistort
raise Exception('dwifslpreproc failed, please look above for '
Exception: dwifslpreproc failed, please look above for error sources.
(DKE) [blab@localhost Scans]$

[TheJaeger]

FSL's eddy only works with CUDA 10.0 if you have an Nvidia GPU. You need to get uninstall CUDA 10.2 and install CUDA 10.0 in its place. if you don't have a CUDA-enabled GPU, then resolve missing libquadmath.so.0 library by installing gcc.

[TheJaeger]

You can check your current Nvidia driver and CUDA versions with

nvidia-smi
nvcc -V

Refer to instructions here or here on how to install specific CUDA version on CentOS. There are countless other instructions you may refer to across the web.

Just be sure that you have a CUDA-enabled GPU physically present in your computer before you begin troubleshooting.

[mmsarhan]

I figured out that i do not have CUDA on my computer and downloaded GCC. I checked the version and it say I downloaded version 4.8.5. Is there anything else I need to install so that the DKI processing will work?

[TheJaeger]

Give it a shot again to see if it resolved the error.

[TheJaeger]

If it's still a problem, I suggest running the NeuroDock container. It should theoretically give you better performance than a VM and is guaranteed to run flawlessly.

[mmsarhan]

@TheJaeger
I tried running neurodock, but I am not sure the installation went correctly. I was able to download the Docker for Windows application, but when I went to go to the terminal and try to download neurodocks and received this error message:
error response from daemon manifest for dmri/neurodock:v0.2 not found: manifest unknown: manifest unknown