-proc_func command operation problem

[wangzx963]

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

functional MRI processing
	micapipe v0.2.3 'Northern flicker', container_micapipe-v0.2.3 

-------------------------------------------------------------�[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