search

MICA-MNI / micapipe

micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below
http://micapipe.readthedocs.io
GNU General Public License v3.0
80 stars 27 forks source link

Bug: mrdegibbs (and dwifslpreproc later) fails in 0.1.5 #64

Closed araikes closed 1 year ago

araikes commented 1 year ago

Pulled and built a docker/singularity image for 0.1.5. Structural and Freesurfer appear to run fine. However, running into issues with -proc_dwi

Call:

singularity run --cleanenv -B ${PWD}/nifti:/nifti:ro -B ${PWD}/derivatives/micapipe:/output -B /groups/adamraikes/license.txt:/opt/freesurfer-6.0.0/license.txt -B /tmp:/tmp /groups/adamraikes/singularity_images/micapipe_0.1.5.sif -bids /nifti -out /output -sub 00228190 -ses 00 -proc_dwi -dwi_main /nifti/sub-00228190/ses-00/dwi/sub-00228190_ses-00_dir-AP_dwi.nii.gz -b0thr 61

Error:

COMMAND -->   mrdegibbs /tmp/10672_micapipe_proc-dwi_00228190/MP-PCA_dwi.mif  -nthreads 6  
mrdegibbs: [ERROR] Expected exactly 2 arguments (1 supplied)
mrdegibbs: [ERROR] Usage: mrdegibbs in out
mrdegibbs: [ERROR] Yours: mrdegibbs /tmp/10672_micapipe_proc-dwi_00228190/MP-PCA_dwi.mif
mrcalc: [ERROR] Could not interpret string "" as either an image path or a numerical value
mrcalc: [ERROR] As image: 
mrcalc: [ERROR] no name supplied to open image!
mrcalc: [ERROR] As numerical value: 
mrcalc: [ERROR] cannot convert empty string to complex float
mrmath: [ERROR] no filename supplied to standard input (broken pipe?)
mrmath: [ERROR] error opening image "-"

Looks like $dns_dwi is never defined https://github.com/MICA-MNI/micapipe/blob/23a5215e7525f4cbbb7b44d5ee7208cf80d918e2/functions/02_proc-dwi.sh#L198

araikes commented 1 year ago

I fixed this locally by re-adding the path definition for dns_dwi from 0.1.4 and it works to completion.

However, QC no longer works in its entirety. Namely, some files are being written as .nii.gz instead of .mif files. Addtionally, the denoising and deGibbsing residual files are being written to ${tmp} rather than ${proc_dwi}.

Update: -SC doesn't work either, as it's looking for model-DTI_FA.mif to validate that -proc_dwi is done whereas it is now model-DTI_FA.nii.gz

adamraikes @ r2u28n1.puma.hpc.arizona.edu Tue Feb 21 11:34:51 MST 2023:
COMMAND -->   mrconvert /xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-00/dwi/sub-00228190_ses-00_space-dwi_desc-MP-PCA_residuals-dwi.mif /tmp/dwi_res.nii.gz  
mrconvert: [ERROR] failed to open key/value file "/xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-00/dwi/sub-00228190_ses-00_space-dwi_desc-MP-PCA_residuals-dwi.mif": No such file or directory
mrconvert: [ERROR] error opening image "/xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-00/dwi/sub-00228190_ses-00_space-dwi_desc-MP-PCA_residuals-dwi.mif"

adamraikes @ r2u28n1.puma.hpc.arizona.edu Tue Feb 21 11:34:51 MST 2023:
COMMAND -->   mrconvert /xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-00/dwi/sub-00228190_ses-00_space-dwi_desc-deGibbs_residuals-dwi.mif /tmp/dwi_deGibbs.nii.gz  
mrconvert: [ERROR] failed to open key/value file "/xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-00/dwi/sub-00228190_ses-00_space-dwi_desc-deGibbs_residuals-dwi.mif": No such file or directory
mrconvert: [ERROR] error opening image "/xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-00/dwi/sub-00228190_ses-00_space-dwi_desc-deGibbs_residuals-dwi.mif"

adamraikes @ r2u28n1.puma.hpc.arizona.edu Tue Feb 21 11:34:51 MST 2023:
COMMAND -->   mrmath /xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-00/dwi/sub-00228190_ses-00_space-dwi_desc-dwi_preproc.mif mean /tmp/dwi_corr.nii.gz -axis 3  
mrmath: [100%] preloading data for "/xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-00/dwi/sub-00228190_ses-00_space-dwi_desc-dwi_preproc.mif"
mrmath: [100%] computing mean along axis 3...
mrmath: [100%] compressing image "/tmp/dwi_corr.nii.gz"

adamraikes @ r2u28n1.puma.hpc.arizona.edu Tue Feb 21 11:34:51 MST 2023:
COMMAND -->   mrconvert /xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-00/dwi/sub-00228190_ses-00_space-dwi_model-CSD_map-FOD_desc-wmNorm.mif -coord 3 0 -axes 0,1,2 /tmp/dwi_fod.nii.gz  
mrconvert: [100%] copying from "/xdisk/ada...CSD_map-FOD_desc-wmNorm.mif" to "/tmp/dwi_fod.nii.gz"
mrconvert: [100%] compressing image "/tmp/dwi_fod.nii.gz"

adamraikes @ r2u28n1.puma.hpc.arizona.edu Tue Feb 21 11:34:52 MST 2023:
COMMAND -->   mrconvert /xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-00/dwi/sub-00228190_ses-00_space-dwi_desc-gmwmi-mask.mif /tmp/dwi_gmwmi.nii.gz  
mrconvert: [100%] copying from "/xdisk/ada...ace-dwi_desc-gmwmi-mask.mif" to "/tmp/dwi_gmwmi.nii.gz"
mrconvert: [100%] compressing image "/tmp/dwi_gmwmi.nii.gz"

adamraikes @ r2u28n1.puma.hpc.arizona.edu Tue Feb 21 11:34:52 MST 2023:
COMMAND -->   mrconvert /xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-00/dwi/sub-00228190_ses-00_space-dwi_desc-iFOD1-1M_tdi.mif /tmp/dwi_tdi.nii.gz  
mrconvert: [100%] copying from "/xdisk/ada...e-dwi_desc-iFOD1-1M_tdi.mif" to "/tmp/dwi_tdi.nii.gz"
mrconvert: [100%] compressing image "/tmp/dwi_tdi.nii.gz"

adamraikes @ r2u28n1.puma.hpc.arizona.edu Tue Feb 21 11:34:52 MST 2023:
COMMAND -->   mrmath /tmp/dwi_tdi.nii.gz mean /tmp/dwi_tdi_mean.nii.gz -axis 3  
mrmath: [100%] uncompressing image "/tmp/dwi_tdi.nii.gz"
mrmath: [100%] preloading data for "/tmp/dwi_tdi.nii.gz"
mrmath: [100%] computing mean along axis 3...
mrmath: [100%] compressing image "/tmp/dwi_tdi_mean.nii.gz"

adamraikes @ r2u28n1.puma.hpc.arizona.edu Tue Feb 21 11:34:52 MST 2023:
COMMAND -->   mrconvert /xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-00/dwi/sub-00228190_ses-00_space-dwi_model-DTI_map-ADC.mif /tmp/dwi_adc.nii.gz  
mrconvert: [ERROR] failed to open key/value file "/xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-00/dwi/sub-00228190_ses-00_space-dwi_model-DTI_map-ADC.mif": No such file or directory
mrconvert: [ERROR] error opening image "/xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-00/dwi/sub-00228190_ses-00_space-dwi_model-DTI_map-ADC.mif"

adamraikes @ r2u28n1.puma.hpc.arizona.edu Tue Feb 21 11:34:52 MST 2023:
COMMAND -->   mrconvert /xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-00/dwi/sub-00228190_ses-00_space-dwi_model-DTI_map-FA.mif /tmp/dwi_fa.nii.gz  
mrconvert: [ERROR] failed to open key/value file "/xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-00/dwi/sub-00228190_ses-00_space-dwi_model-DTI_map-FA.mif": No such file or directory
mrconvert: [ERROR] error opening image "/xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-00/dwi/sub-00228190_ses-00_space-dwi_model-DTI_map-FA.mif"

adamraikes @ r2u28n1.puma.hpc.arizona.edu Tue Feb 21 11:34:52 MST 2023:
COMMAND -->   mrconvert /xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-00/dwi/sub-00228190_ses-00_space-dwi_desc-5tt.nii.gz -coord 3 0 -axes 0,1,2 /tmp/dwi_5tt.nii.gz  
mrconvert: [100%] uncompressing image "/xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-00/dwi/sub-00228190_ses-00_space-dwi_desc-5tt.nii.gz"
mrconvert: [100%] copying from "/xdisk/ada...0_space-dwi_desc-5tt.nii.gz" to "/tmp/dwi_5tt.nii.gz"
mrconvert: [100%] compressing image "/tmp/dwi_5tt.nii.gz"

[ INFO ]..... DWI MP-PCA mean residuals (mean) 

[ INFO ]..... DWI Ring Gibbs mean residuals (mean) 

[ INFO ]..... DWI b0 pre-processed
araikes commented 1 year ago

@rcruces, are you all open to PRs on this project to fix the above issues as well as some other now out of date things? (e.g., /opt/micapipe/functions/01_proc-struc_volumetric.sh: line 142: json_nativepro_t1w: command not found because its now json_nativepro_T1w)

rcruces commented 1 year ago

If you are still interest, please start a pull request to our branch v0.1.5 https://github.com/MICA-MNI/micapipe/tree/micapipe_v0.1.5.

However, we greatly encourage all our users to try the newest version of the pipeline v0.2.0 Northern Flicker

https://github.com/MICA-MNI/micapipe/releases/tag/v0.2.0