Problem with dwiintensitynorm

1

Hello all,
I am trying to implement Fibre density and cross-section - Single-tissue CSD pipeline on a Linux based cluster.
Here is the OS and MRtrix version that I’m using:

Linux node8.cluster 3.10.0-693.11.6.el7.x86_64 #1 SMP Thu Jan 4 01:06:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

MRtrix 3.0_RC2-10-g7b4c28ab dwiintensitynorm bin version: 3.0_RC2-10-g7b4c28ab

My diffusion data were collected on a Siemens 3T Tim Trio and has 6 b0 volumes followed by 61 diffusion volumes.

I converted the nifiti files to mif format using the mrconvert command.

After running the following command:

dwiintensitynorm $1/dwiintensitynorm/dwi_input/ $1/dwiintensitynorm/mask_input/ $1/dwiintensitynorm/dwi_output/ $1/dwiintensitynorm/fa_template.nii.gz $1/dwiintensitynorm/fa_template_wm_mask.nii.gz

I receive this error:

dwiintensitynorm:
dwiintensitynorm: [ERROR] Command failed: dwinormalise /home/data/dwiintensitynorm/dwi_input/00039-03-02_CSI20160108.mif wm_mask_warped/00039-03-02_CSI20160108.mif /home/data/dwiintensitynorm/dwi_output/00039-03-02_CSI20160108.mif (dwiintensitynorm:102)
dwiintensitynorm: Output of failed command:
dwinormalise: computing 50th percentile within mask...  [==================================================]

dwinormalise: [SYSTEM FATAL CODE: SIGSEGV (11)] Segmentation fault: Invalid memory access
dwiintensitynorm: Changing back to original directory (/home/data)
dwiintensitynorm: Script failed while executing the command: dwinormalise /home/data/dwiintensitynorm/dwi_input/00039-03-02_CSI20160108.mif wm_mask_warped/00039-03-02_CSI20160108.mif /home/data/dwiintensitynorm/dwi_output/00039-03-02_CSI20160108.mif
dwiintensitynorm: For debugging, inspect contents of temporary directory: /home/data/dwiintensitynorm-tmp-KI8710/

Any idea what’s going wrong?

PS: I tried to run dwiintensitynorm with - debug - nthread 0 switches but after 3 days of running it was still running and I had to give up.

Thank you,
Mahmoud

2

As an update, I could finally get some results out of the dwiintensitnorm by removing some of the subjects but the output FA template does not seem to be right and it’s kinda skewed.

FA_Template
FA_Template.PNG1916×844 26 KB

I appreciate any comments as I stopped at this step for a long time.

Thanks,
Mahmoud

3

Looks like a registration problem, which is usually caused by a problem with the data. Usual suspects are artefacts in DWI data, bad masks or the absence of masks. Have a look at the FA images in the subfolder fa in your temporary directory dwiintensitynorm-tmp-* and at the transformed images and masks in the subfolder population_template. You can do this while the script is running.

The segfault in dwinormalise is a bug that might be related to the poor registration. Have a look at /home/data/dwiintensitynorm/dwi_input/00039-03-02_CSI20160108.mif and wm_mask_warped/00039-03-02_CSI20160108.mif /home/data/dwiintensitynorm/dwi_output/00039-03-02_CSI20160108.mif

You can count voxels in each mask with mrstats path_to_dwiintensitynorm-tmp/wm_mask_warped/*.mif -ignorezero -output count or just use mrview to go through them.