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bids-apps / MRtrix3_connectome

Generate subject connectomes from raw BIDS data & perform inter-subject connection density normalisation, using the MRtrix3 software package.
http://www.mrtrix.org/
Apache License 2.0
50 stars 26 forks source link

Upgrade to 0.6.0 #126

Open Lestropie opened 1 year ago

Lestropie commented 1 year ago

Had to address #123 due to it precluding processing of data in my own lab.

Results in increment to version 0.6.0 as the incorporation of dwicat will result in a change in behaviour even for data that previously would have processed to completion.

On MRtrix3 I have created a branch off of 3.0.4 with a single commit that cherry-picks https://github.com/MRtrix3/mrtrix3/pull/2702 off of dev. Makes the behaviour of that software dependency a little more reportable.

@aaroncapon Do you want to try building a container with this code (and the updated MRtrix3 dependency) and make sure it runs before I merge & tag? CI is completely broken here, repo is highly neglected, so independent verification would be good if not onerous.

aaroncapon commented 1 year ago

Hi. Thanks for all this work @Lestropie! I should get a chance to build the container today or tomorrow. Will report back with the results.

aaroncapon commented 1 year ago

Unfortunately, there was an issue during processing using the new code. Below is the error message.

Command: mrconvert dwi2_denoised_mag_degibbs.mif dwi2_denoised_mag_degibbs_bzero.mif -coord 3 0,1 Command: mrcat [dwi*_denoised_mag_degibbs_bzero.mif (2 items)] dwifslpreproc_seepi.mif -axis 3 mrtrix3_connectome.py: Performing various geometric corrections of DWIs Command: dwifslpreproc dwifslpreproc_in.mif dwifslpreproc_out.mif -se_epi dwifslpreproc_seepi.mif -eddy_options " --repol" -rpe_header -eddyqc_text eddyqc/ Command: mrmath dwifslpreproc_out.mif max -axis 3 - | mrthreshold - dwi_validdata_mask.mif -abs 0.0 -comparison gt mrtrix3_connectome.py: Performing intial DWI brain masking Command: dwi2mask dwifslpreproc_out.mif dwi_mask_init.mif

mrtrix3_connectome.py: [ERROR] dwi2mask dwifslpreproc_out.mif dwi_mask_init.mif (mrtrix3_connectome.py:1508) mrtrix3_connectome.py: [ERROR] Information from failed command: mrtrix3_connectome.py:

Error: argument algorithm: invalid choice: 'dwifslpreproc_out.mif' (choose from '3dautomask', 'ants', 'b02template', 'consensus', 'fslbet', 'hdbet', 'legacy', 'mean', 'mtnorm', 'synthstrip', 'trace') Usage: dwi2mask algorithm [ options ] ... (Run dwi2mask -help for more information)

mrtrix3_connectome.py: mrtrix3_connectome.py: [ERROR] For debugging, inspect contents of scratch directory: /dwi_scratch/dwi2adc/9UG34Y/mrtrix3_connectome.py-tmp-GFCYVU/ mrtrix3_connectome.py: Scratch directory retained; location: /dwi_scratch/dwi2adc/9UG34Y/mrtrix3_connectome.py-tmp-GFCYVU

As I said yesterday, this can be low priority as the subject that encountered this issue has already been sent for assessment.