micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below
Display Main phase scan: file not found at run time
docker run --rm ^
-v "E:\QTAB\data\ds004146-download:/bids" ^
-v "E:\QTAB\output:/out" ^
-v "E:\QTAB\tmp:/tmp" ^
-v "E:\QTAB\license.txt:/opt/licence.txt" ^
--cpus=9 ^
--memory=20g ^
micalab/micapipe:v0.2.3 ^
-bids /bids -out /out -fs_licence /opt/licence.txt ^
-sub sub-0037 -ses 01 ^
-proc_structural ^
-proc_surf ^
-post_structural ^
-proc_func ^
-func_pe /bids/sub-0037/ses-01/func/sub-0037_ses-01_task-rest_acq-APse_bold.nii.gz ^
-func_rpe /bids/sub-0037/ses-01/func/sub-0037_ses-01_task-rest_acq-PAse_bold.nii.gz ^
-dropTR 5 ^
-mainScanStr task-rest_acq-APse_bold ^
-QC_subj
the logs：
/opt/micapipe/functions/02_proc-func.sh: line 85: subject_dir: command not found
[38;5;75m
[ INFO ]..... Inputs: [0m
Topup Config : [38;5;122mDEFAULT[0m
ICA fix training : [38;5;122mDEFAULT[0m
Main scan : [38;5;122mDEFAULT[0m
Phase scan : [38;5;122m/home/mica/E:\QTAB\data\ds004146-download\sub-0037\ses-01 unc\sub-0037_ses-01_task-rest_acq-AP_bold.nii.gz[0m
Reverse Phase : [38;5;122m/home/mica/E:\QTAB\data\ds004146-download\sub-0037\ses-01 unc\sub-0037_ses-01_task-rest_acq-PA_bold.nii.gz[0m
Perform NSR : [38;5;122m0[0m
Perform GSR : [38;5;122m0[0m
No FIX : [38;5;122m0[0m
Longitudinal ses : [38;5;122mFALSE[0m
Drop TR : [38;5;122mTRUE[0m
Surface : [38;5;122mfastsurfer[0m
[38;5;75m
[ INFO ]..... No run number specified for func scan and did not find more than one run for main scan - all good! [0m
[38;5;75m
[ INFO ]..... Using default json scan: /bids/sub-0037/ses-01/func/sub-0037_ses-01_task-rest_acq-AP_bold.json [0m
[38;5;75m
[ INFO ]..... No run number specified for phase reversals and did not find more than one phase reversal scan - all good! [0m
[38;5;184m
[ WARNING ]..... Subject 0037 doesn't have a Main Phase Scan (pe): TOPUP will run only if a rpe is provided [0m
[38;5;184m
[ WARNING ]..... Subject 0037 doesn't have Reverse Phase Scan (rpe): TOPUP will be skipped [0m
[38;5;75m
[ INFO ]..... Will use default config file for TOPUP: /opt/fsl-6.0.2/etc/flirtsch/b02b0_1.cnf [0m
[38;5;75m
[ INFO ]..... ICA-FIX pipeline will be run! [0m
[38;5;75m
[ INFO ]..... Will use default training file for ICA-FIX: /opt/micapipe/functions/MICAMTL_training_15HC_15PX.RData [0m
[38;5;75m
[ INFO ]..... Global, white matter and CSF signal regression will not be performed (default) [0m
Display Main phase scan: file not found at run time docker run --rm ^ -v "E:\QTAB\data\ds004146-download:/bids" ^ -v "E:\QTAB\output:/out" ^ -v "E:\QTAB\tmp:/tmp" ^ -v "E:\QTAB\license.txt:/opt/licence.txt" ^ --cpus=9 ^ --memory=20g ^ micalab/micapipe:v0.2.3 ^ -bids /bids -out /out -fs_licence /opt/licence.txt ^ -sub sub-0037 -ses 01 ^ -proc_structural ^ -proc_surf ^ -post_structural ^ -proc_func ^ -func_pe /bids/sub-0037/ses-01/func/sub-0037_ses-01_task-rest_acq-APse_bold.nii.gz ^ -func_rpe /bids/sub-0037/ses-01/func/sub-0037_ses-01_task-rest_acq-PAse_bold.nii.gz ^ -dropTR 5 ^ -mainScanStr task-rest_acq-APse_bold ^ -QC_subj
the logs： /opt/micapipe/functions/02_proc-func.sh: line 85: subject_dir: command not found [38;5;75m [ INFO ]..... Inputs: [0m Topup Config : [38;5;122mDEFAULT[0m ICA fix training : [38;5;122mDEFAULT[0m Main scan : [38;5;122mDEFAULT[0m Phase scan : [38;5;122m/home/mica/E:\QTAB\data\ds004146-download\sub-0037\ses-01 unc\sub-0037_ses-01_task-rest_acq-AP_bold.nii.gz[0m Reverse Phase : [38;5;122m/home/mica/E:\QTAB\data\ds004146-download\sub-0037\ses-01 unc\sub-0037_ses-01_task-rest_acq-PA_bold.nii.gz[0m Perform NSR : [38;5;122m0[0m Perform GSR : [38;5;122m0[0m No FIX : [38;5;122m0[0m Longitudinal ses : [38;5;122mFALSE[0m Drop TR : [38;5;122mTRUE[0m Surface : [38;5;122mfastsurfer[0m [38;5;75m [ INFO ]..... No run number specified for func scan and did not find more than one run for main scan - all good! [0m [38;5;75m [ INFO ]..... Using default json scan: /bids/sub-0037/ses-01/func/sub-0037_ses-01_task-rest_acq-AP_bold.json [0m [38;5;75m [ INFO ]..... No run number specified for phase reversals and did not find more than one phase reversal scan - all good! [0m [38;5;184m [ WARNING ]..... Subject 0037 doesn't have a Main Phase Scan (pe): TOPUP will run only if a rpe is provided [0m [38;5;184m [ WARNING ]..... Subject 0037 doesn't have Reverse Phase Scan (rpe): TOPUP will be skipped [0m [38;5;75m [ INFO ]..... Will use default config file for TOPUP: /opt/fsl-6.0.2/etc/flirtsch/b02b0_1.cnf [0m [38;5;75m [ INFO ]..... ICA-FIX pipeline will be run! [0m [38;5;75m [ INFO ]..... Will use default training file for ICA-FIX: /opt/micapipe/functions/MICAMTL_training_15HC_15PX.RData [0m [38;5;75m [ INFO ]..... Global, white matter and CSF signal regression will not be performed (default) [0m
[38;5;141m
-------------------------------------------------------------[0m [38;5;75m [ INFO ]..... MICA pipe - Software versions [0m MRtrix3..... [38;5;122m3.0.1[0m [38;5;122m/opt/miniconda-22.11.1/envs/micapipe/bin/mrinfo[0m FSL......... [38;5;122m6.0[0m [38;5;122m/opt/fsl-6.0.2[0m ANFI........ [38;5;122m Jun 23 2023 (Version AFNI_23.1.09 'Publius Helvius Pertinax')[0m [38;5;122m/opt/afni-latest/3dresample[0m ANTS........ [38;5;122m 2.3.3.dev168-g29bdf[0m [38;5;122m/opt/ants-2.3.4/[0m WorkBench... [38;5;122m1.3.2[0m [38;5;122m/usr/bin/wb_command[0m FreeSurfer.. [38;5;122mfreesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275[0m [38;5;122m/opt/freesurfer-7.3.2[0m fix......... [38;5;122m/opt/fix1.068/fix[0m [38;5;122m/opt/fix1.068[0m python...... [38;5;122m3.9.18[0m [38;5;122m/opt/miniconda-22.11.1/envs/micapipe/bin/python[0m R........... [38;5;122m3.6.3[0m [38;5;122m/usr/bin/R[0m conda....... [38;5;122mconda 22.11.1[0m [38;5;122m/opt/miniconda-22.11.1/condabin/conda[0m [38;5;75m [ INFO ]..... Variables for functional processing [0m T1 nativepro : [38;5;122m/out/micapipe_v0.2.0/sub-0037/ses-01/anat/sub-0037_ses-01_space-nativepro_T1w.nii.gz[0m T1 surface : [38;5;122m/out/fastsurfer/sub-0037_ses-01/mri/orig.mgz[0m mainScan : [38;5;122m/bids/sub-0037/ses-01/func/sub-0037_ses-01_task-rest_acq-AP_bold.nii.gz[0m mainScan json : [38;5;122m/bids/sub-0037/ses-01/func/sub-0037_ses-01_task-rest_acq-AP_bold.json[0m Main phase scan : [38;5;122mfile not found[0m Main reverse phase : [38;5;122mfile not found[0m TOPUP config file : [38;5;122m/opt/fsl-6.0.2/etc/flirtsch/b02b0_1.cnf[0m ICA-FIX training : [38;5;122m/opt/micapipe/functions/MICAMTL_training_15HC_15PX.RData[0m Saving temporal dir: [38;5;122mFALSE[0m Parallel processing : [38;5;122m6 threads[0m proc_fun outputs: [38;5;122m/out/micapipe_v0.2.0/sub-0037/ses-01/func/desc-se_task-rest_acq-AP_bold[0m tagMRI: [38;5;122mse_task-rest_acq-AP_bold[0m