dwibiascorrect: error when using the `-debug` flag

[sebastientourbier]

The bug

Running dwibiascorrect with option flag -debug raises error.

To Reproduce

Command:

/home/localadmin/Softwares/miniconda3/bin/dwibiascorrect ants -mask /home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/flirt_dwimask/dwi_brain_mask.nii.gz -bias diffusion_denoised_biasfield.mif -debug -force /home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/dwi_denoise/diffusion_denoised.mif /home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/dwi_biascorrect/diffusion_denoised_biascorr.mif

Terminal output:

dwibiascorrect: 
dwibiascorrect: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the help page (-help option) for more information.
dwibiascorrect: 
dwibiascorrect: [DEBUG] path.script_subdir_name() (from algorithm.py:69): dwibiascorrect
dwibiascorrect: [WARNING] Output file 'diffusion_denoised_biasfield.mif' already exists; will be overwritten at script completion
dwibiascorrect: Generated scratch directory: /home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/
dwibiascorrect: [DEBUG] path.from_user() (from dwibiascorrect:50): /home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/dwi_denoise/diffusion_denoised.mif -> /home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/dwi_denoise/diffusion_denoised.mif
dwibiascorrect: [DEBUG] path.to_scratch() (from dwibiascorrect:50): in.mif -> /home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/in.mif
dwibiascorrect: [DEBUG] run.exe_name() (from run.py:546): mrconvert -> mrconvert
dwibiascorrect: [DEBUG] run.version_match() (from run.py:330): Version-matched executable for mrconvert: /home/localadmin/Softwares/miniconda3/bin/mrconvert
dwibiascorrect: [DEBUG] run._shebang() (from run.py:340): File "/home/localadmin/Softwares/miniconda3/bin/mrconvert": Not a text file
dwibiascorrect: [DEBUG] run.command() (from dwibiascorrect:50): To execute: [['/home/localadmin/Softwares/miniconda3/bin/mrconvert', '/home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/dwi_denoise/diffusion_denoised.mif', '/home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/in.mif', '-info']]
Command:  mrconvert /home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/dwi_denoise/diffusion_denoised.mif /home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/in.mif
          mrconvert: [INFO] opening image "/home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/dwi_denoise/diffusion_denoised.mif"...
          mrconvert: [INFO] image "/home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/dwi_denoise/diffusion_denoised.mif" opened with dimensions 96x96x38x129, voxel spacing 2.2083300000000001x2.2083300000000001x3x5.9000000000000004, datatype Float32LE
          mrconvert: [INFO] found 129x4 diffusion gradient table
          mrconvert: [INFO] creating image "/home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/in.mif"...
          mrconvert: [INFO] image "/home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/in.mif" created with dimensions 96x96x38x129, voxel spacing 2.2083300000000001x2.2083300000000001x3x5.9000000000000004, datatype Float32LE
          mrconvert: [100%] copying from "/home/loca...oise/diffusion_denoised.mif" to "/home/loca...ascorrect-tmp-XEGOZD/in.mif"
dwibiascorrect: [DEBUG] path.from_user() (from dwibiascorrect:52): /home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/flirt_dwimask/dwi_brain_mask.nii.gz -> /home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/flirt_dwimask/dwi_brain_mask.nii.gz
dwibiascorrect: [DEBUG] path.to_scratch() (from dwibiascorrect:52): mask.mif -> /home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/mask.mif
dwibiascorrect: [DEBUG] run.exe_name() (from run.py:546): mrconvert -> mrconvert
dwibiascorrect: [DEBUG] run.version_match() (from run.py:330): Version-matched executable for mrconvert: /home/localadmin/Softwares/miniconda3/bin/mrconvert
dwibiascorrect: [DEBUG] run._shebang() (from run.py:340): File "/home/localadmin/Softwares/miniconda3/bin/mrconvert": Not a text file
dwibiascorrect: [DEBUG] run.command() (from dwibiascorrect:52): To execute: [['/home/localadmin/Softwares/miniconda3/bin/mrconvert', '/home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/flirt_dwimask/dwi_brain_mask.nii.gz', '/home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/mask.mif', '-datatype', 'bit', '-info']]
Command:  mrconvert /home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/flirt_dwimask/dwi_brain_mask.nii.gz /home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/mask.mif -datatype bit
          mrconvert: [INFO] opening image "/home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/flirt_dwimask/dwi_brain_mask.nii.gz"...
          mrconvert: [INFO] image "/home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/flirt_dwimask/dwi_brain_mask.nii.gz" opened with dimensions 96x96x38, voxel spacing 2.2083332538604736x2.2083332538604736x3, datatype Float32LE
          mrconvert: [INFO] no valid diffusion gradient table found
          mrconvert: [INFO] error importing diffusion gradient table for image "/home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/flirt_dwimask/dwi_brain_mask.nii.gz"
          mrconvert: [100%] uncompressing image "/home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/flirt_dwimask/dwi_brain_mask.nii.gz"
          mrconvert: [INFO] creating image "/home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/mask.mif"...
          mrconvert: [INFO] image "/home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/mask.mif" created with dimensions 96x96x38, voxel spacing 2.2083332538604736x2.2083332538604736x3, datatype Bit
          mrconvert: [100%] copying from "/home/loca...imask/dwi_brain_mask.nii.gz" to "/home/loca...correct-tmp-XEGOZD/mask.mif"
dwibiascorrect: Changing to scratch directory (/home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/)
dwibiascorrect: [DEBUG] path.name_temporary() (from image.py:33): /home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/mrtrix-tmp-ti2iWL.json
dwibiascorrect: [DEBUG] run.exe_name() (from run.py:546): mrinfo -> mrinfo
dwibiascorrect: [DEBUG] run.version_match() (from image.py:34): Version-matched executable for mrinfo: /home/localadmin/Softwares/miniconda3/bin/mrinfo
dwibiascorrect: [DEBUG] run.exe_name() (from image.py:34): /home/localadmin/Softwares/miniconda3/bin/mrinfo -> /home/localadmin/Softwares/miniconda3/bin/mrinfo
dwibiascorrect: Loading header for image file 'in.mif'
dwibiascorrect: [DEBUG] image.__init__() (from dwibiascorrect:59): ['/home/localadmin/Softwares/miniconda3/bin/mrinfo', 'in.mif', '-json_all', '/home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/mrtrix-tmp-ti2iWL.json']
dwibiascorrect: [DEBUG] image.__init__() (from dwibiascorrect:59): {'_name': 'in.mif', '_size': [96, 96, 38, 129], '_spacing': [2.20833, 2.20833, 3.0, 5.9], '_strides': [1, 2, 3, 4], '_format': 'MRtrix', '_datatype': 'Float32LE', '_intensity_offset': 0.0, '_intensity_scale': 1.0, '_transform': [[0.999999943880058, 5.33884694434427e-08, 0.000335022184972424, -102.900541691394], [1.57276657824972e-05, 0.998889975305693, -0.0471043187585057, -93.3131521331962], [-0.000334652837870155, 0.0471043228779298, 0.998889919317656, -23.3364965748897], [0.0, 0.0, 0.0, 1.0]], '_keyval': {'command_history': ["mrconvert -stride '1,2,3,4' -force -fslgrad /output_dir/cmp/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bvec /output_dir/cmp/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bval -quiet /output_dir/cmp/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.nii.gz diffusion.mif  (version=3.0.2)", 'dwidenoise -mask /output_dir/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/flirt_dwimask/dwi_brain_mask.nii.gz -noise diffusion_noisemap.mif -force -debug /output_dir/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert/diffusion.mif diffusion_denoised.mif  (version=3.0.2)', '/home/localadmin/Softwares/miniconda3/bin/mrconvert /home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/dwi_denoise/diffusion_denoised.mif /home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/in.mif -info  (version=3.0.2)'], 'comments': 'TE=1e+02;Time=160316.967;phase=1', 'dw_scheme': [[0.0, 0.0, 0.0, 0.0], [4.604794858e-11, -0.9999980001, -0.001999937115, 500.0], [1.455731894e-10, 2.590861083e-08, -1.0, 500.0], [-0.999998, -9.949299793e-11, -0.001999989269, 500.0], [0.7071057544, -0.7071063938, -0.00141422849, 1000.0], [0.7067542777, -5.561829258e-08, -0.707459109, 1000.0], [2.6698783e-10, -0.7067539959, -0.7074593906, 1000.0], [1.98246735e-10, 0.7067540551, -0.7074593314, 1000.0], [-0.7071061444, -0.7071060037, -0.001414231861, 1000.0], [-0.7067538111, 4.064903066e-08, -0.7074595752, 1000.0], [0.5770938972, -0.5770939732, -0.577862596, 1500.0], [0.5770936909, 0.5770944823, -0.5778622937, 1500.0], [-0.5770942262, -0.5770936115, -0.5778626287, 1500.0], [-0.5770938222, 0.5770937722, -0.5778628717, 1500.0], [4.701760879e-11, -0.999999875, -0.0004999499268, 2000.0], [1.455731894e-10, 2.590861083e-08, -1.0, 2000.0], [-0.999999875, -6.189255252e-11, -0.0004999995985, 2000.0], [0.8944271678, -0.44721332, -0.0005366216217, 2500.0], [0.8942481999, 1.233911471e-09, -0.4475713987, 2500.0], [0.4472140294, -0.894426813, -0.0005366778619, 2500.0], [0.447141854, -6.331739179e-08, -0.8944630581, 2500.0], [6.047983974e-10, -0.8942484278, -0.4475709434, 2500.0], [-1.547638207e-10, -0.4471420937, -0.8944629383, 2500.0], [6.038469206e-11, 0.4471424734, -0.8944627485, 2500.0], [-2.987575823e-10, 0.8942483962, -0.4475710065, 2500.0], [-0.4472142273, -0.8944267141, -0.0005366223904, 2500.0], [-0.4471422325, 2.979426711e-09, -0.894462869, 2500.0], [-0.8944272642, -0.4472131271, -0.0005366111842, 2500.0], [-0.8942481864, -1.203342597e-08, -0.4475714257, 2500.0], [0.8163150495, -0.4082259566, -0.4086334645, 3000.0], [0.8163149864, 0.4082255761, -0.4086339707, 3000.0], [0.4082262058, -0.816314944, -0.4086334263, 3000.0], [0.4081581457, -0.408157277, -0.816587145, 3000.0], [0.408157348, 0.4081578487, -0.8165872579, 3000.0], [0.4082253801, 0.8163154, -0.4086333403, 3000.0], [-0.4082260024, -0.8163148249, -0.4086338675, 3000.0], [-0.4081577425, -0.408157098, -0.816587436, 3000.0], [-0.4081578271, 0.4081579636, -0.816586961, 3000.0], [-0.4082254286, 0.8163152063, -0.4086336787, 3000.0], [-0.8163152896, -0.4082256582, -0.408633283, 3000.0], [-0.8163150614, 0.4082255313, -0.4086338657, 3000.0], [0.7071071135, -0.7071063605, -0.0003535496407, 4000.0], [0.7069299418, -5.319339341e-09, -0.7072835764, 4000.0], [-9.789377913e-11, -0.7069302433, -0.707283275, 4000.0], [1.567798364e-10, 0.7069298265, -0.7072836916, 4000.0], [-0.7071066491, -0.7071068248, -0.0003535998457, 4000.0], [-0.7069299747, 3.830753602e-08, -0.7072835434, 4000.0], [0.6665928365, -0.6665925637, -0.3336290519, 4500.0], [0.6664856674, -0.3333169916, -0.6668557852, 4500.0], [0.6664856527, 0.3333167604, -0.6668559155, 4500.0], [0.6665929437, 0.6665923207, -0.3336293233, 4500.0], [0.333317104, -0.6664855564, -0.66685584, 4500.0], [0.3333173941, 0.6664856233, -0.6668556281, 4500.0], [4.085725123e-11, -0.9999999012, -0.0004444170368, 4500.0], [1.455731894e-10, 2.590861083e-08, -1.0, 4500.0], [-0.3333166201, -0.6664858367, -0.6668558017, 4500.0], [-0.3333166057, 0.6664855235, -0.6668561219, 4500.0], [-0.6665924266, -0.666592734, -0.3336295307, 4500.0], [-0.6664858483, -0.3333171152, -0.6668555426, 4500.0], [-0.6664853425, 0.3333167888, -0.6668562113, 4500.0], [-0.6665924202, 0.666592617, -0.3336297773, 4500.0], [-0.9999999012, 3.742696584e-11, -0.0004444399636, 4500.0], [0.9486830278, -0.3162282667, -0.0004427363325, 5000.0], [0.9485630721, 2.321566786e-08, -0.3165882157, 5000.0], [0.3162277787, -0.9486831905, -0.0004427124981, 5000.0], [0.3162084303, -1.470391669e-08, -0.9486897431, 5000.0], [6.094271403e-11, -0.9485631972, -0.3165878406, 5000.0], [3.727802446e-10, -0.3160571874, -0.9487401406, 5000.0], [2.102303804e-10, 0.3162084941, -0.9486897218, 5000.0], [2.418275742e-10, 0.9485631902, -0.3165878617, 5000.0], [-0.3162281986, -0.9486830505, -0.0004427240341, 5000.0], [-0.3162086596, -2.213515469e-08, -0.9486896667, 5000.0], [-0.9486830937, -0.3162280692, -0.0004427716254, 5000.0], [-0.9485632352, -2.792397978e-09, -0.3165877268, 5000.0], [0.9044196305, -0.3014910643, -0.3018745932, 5500.0], [0.9044195348, 0.3014912943, -0.3018746504, 5500.0], [0.3014912367, -0.9044193748, -0.3018751873, 5500.0], [0.3015110819, -0.3013465199, -0.9045890462, 5500.0], [0.3014815607, 0.3014810386, -0.9045540625, 5500.0], [0.301491691, 0.9044192968, -0.3018749673, 5500.0], [-0.3014917901, -0.9044192099, -0.3018751286, 5500.0], [-0.3015110626, -0.3013465021, -0.9045890585, 5500.0], [-0.3014814747, 0.3014810781, -0.904554078, 5500.0], [-0.301491225, 0.904419444, -0.3018749917, 5500.0], [-0.9044195788, -0.3014910964, -0.301874716, 5500.0], [-0.9044196065, 0.3014912379, -0.3018744917, 5500.0], [0.5772539059, -0.577254112, -0.5775427416, 6000.0], [0.5772537687, 0.5772545673, -0.5775424235, 6000.0], [-0.5772541227, -0.5772538622, -0.5775427744, 6000.0], [-0.577254148, 0.5772543081, -0.5775423035, 6000.0], [0.8320501259, -0.5547003438, -0.0003413330173, 6500.0], [0.8319060448, 3.098869511e-08, -0.5549165096, 6500.0], [0.5546999144, -0.8320504122, -0.0003413904583, 6500.0], [0.554572481, -4.940954412e-08, -0.8321354236, 6500.0], [6.072960914e-10, -0.8319059468, -0.5549166565, 6500.0], [-3.666727552e-10, -0.5545724001, -0.8321354776, 6500.0], [2.11767819e-10, 0.5545717321, -0.8321359228, 6500.0], [-3.600334341e-10, 0.831906107, -0.5549164164, 6500.0], [-0.5546999789, -0.8320503692, -0.0003413141108, 6500.0], [-0.5545722601, 2.913643411e-08, -0.8321355709, 6500.0], [-0.832050099, -0.5547003842, -0.0003413181217, 6500.0], [-0.8319060534, 3.281216423e-10, -0.5549164967, 6500.0], [0.8017208664, -0.53446813, -0.2675583495, 7000.0], [0.8016418421, -0.2672396717, -0.5347460283, 7000.0], [0.8016418981, 0.2672394531, -0.5347460537, 7000.0], [0.8017207264, 0.534468159, -0.267558711, 7000.0], [0.5344681068, -0.8017208029, -0.2675585861, 7000.0], [0.53442475, -0.2671552934, -0.8018841786, 7000.0], [0.5343916032, 0.2672533946, -0.8018735795, 7000.0], [0.5344678393, 0.8017210021, -0.2675585238, 7000.0], [0.2672396447, -0.8016419395, -0.5347458958, 7000.0], [0.2672530582, -0.5343914545, -0.8018737907, 7000.0], [0.2672532447, 0.5343918496, -0.8018734652, 7000.0], [0.2672394535, 0.8016416949, -0.534746358, 7000.0], [-0.2672393738, -0.8016420235, -0.5347459053, 7000.0], [-0.2672529745, -0.5343914835, -0.8018737993, 7000.0], [-0.2672527998, 0.534391969, -0.801873534, 7000.0], [-0.2672395729, 0.8016417046, -0.5347462838, 7000.0], [-0.534468046, -0.8017208702, -0.2675585059, 7000.0], [-0.534424298, -0.2671553634, -0.8018844565, 7000.0], [-0.5343916999, 0.2672534444, -0.8018734985, 7000.0], [-0.5344680464, 0.801720919, -0.267558359, 7000.0], [-0.8017210357, -0.5344679886, -0.2675581246, 7000.0], [-0.8016417412, -0.2672397248, -0.5347461531, 7000.0], [-0.8016420535, 0.2672394791, -0.5347458078, 7000.0], [-0.8017211137, 0.5344675679, -0.2675587314, 7000.0], [2.651765635e-12, -0.9999999687, -0.0002500086681, 8000.0], [1.455731894e-10, 2.590861083e-08, -1.0, 8000.0], [-0.9999999687, -1.852948745e-11, -0.0002500002363, 8000.0]], 'mrtrix_version': '3.0.2'}}
dwibiascorrect: [DEBUG] path.name_temporary() (from image.py:33): /home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/mrtrix-tmp-njtCya.json
dwibiascorrect: [DEBUG] run.exe_name() (from run.py:546): mrinfo -> mrinfo
dwibiascorrect: [DEBUG] run.version_match() (from image.py:34): Version-matched executable for mrinfo: /home/localadmin/Softwares/miniconda3/bin/mrinfo
dwibiascorrect: [DEBUG] run.exe_name() (from image.py:34): /home/localadmin/Softwares/miniconda3/bin/mrinfo -> /home/localadmin/Softwares/miniconda3/bin/mrinfo
dwibiascorrect: Loading header for image file 'in.mif'
dwibiascorrect: [DEBUG] image.__init__() (from image.py:175): ['/home/localadmin/Softwares/miniconda3/bin/mrinfo', 'in.mif', '-json_all', '/home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/mrtrix-tmp-njtCya.json']
dwibiascorrect: [DEBUG] image.__init__() (from image.py:175): {'_name': 'in.mif', '_size': [96, 96, 38, 129], '_spacing': [2.20833, 2.20833, 3.0, 5.9], '_strides': [1, 2, 3, 4], '_format': 'MRtrix', '_datatype': 'Float32LE', '_intensity_offset': 0.0, '_intensity_scale': 1.0, '_transform': [[0.999999943880058, 5.33884694434427e-08, 0.000335022184972424, -102.900541691394], [1.57276657824972e-05, 0.998889975305693, -0.0471043187585057, -93.3131521331962], [-0.000334652837870155, 0.0471043228779298, 0.998889919317656, -23.3364965748897], [0.0, 0.0, 0.0, 1.0]], '_keyval': {'command_history': ["mrconvert -stride '1,2,3,4' -force -fslgrad /output_dir/cmp/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bvec /output_dir/cmp/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bval -quiet /output_dir/cmp/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.nii.gz diffusion.mif  (version=3.0.2)", 'dwidenoise -mask /output_dir/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/flirt_dwimask/dwi_brain_mask.nii.gz -noise diffusion_noisemap.mif -force -debug /output_dir/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert/diffusion.mif diffusion_denoised.mif  (version=3.0.2)', '/home/localadmin/Softwares/miniconda3/bin/mrconvert /home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/dwi_denoise/diffusion_denoised.mif /home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/in.mif -info  (version=3.0.2)'], 'comments': 'TE=1e+02;Time=160316.967;phase=1', 'dw_scheme': [[0.0, 0.0, 0.0, 0.0], [4.604794858e-11, -0.9999980001, -0.001999937115, 500.0], [1.455731894e-10, 2.590861083e-08, -1.0, 500.0], [-0.999998, -9.949299793e-11, -0.001999989269, 500.0], [0.7071057544, -0.7071063938, -0.00141422849, 1000.0], [0.7067542777, -5.561829258e-08, -0.707459109, 1000.0], [2.6698783e-10, -0.7067539959, -0.7074593906, 1000.0], [1.98246735e-10, 0.7067540551, -0.7074593314, 1000.0], [-0.7071061444, -0.7071060037, -0.001414231861, 1000.0], [-0.7067538111, 4.064903066e-08, -0.7074595752, 1000.0], [0.5770938972, -0.5770939732, -0.577862596, 1500.0], [0.5770936909, 0.5770944823, -0.5778622937, 1500.0], [-0.5770942262, -0.5770936115, -0.5778626287, 1500.0], [-0.5770938222, 0.5770937722, -0.5778628717, 1500.0], [4.701760879e-11, -0.999999875, -0.0004999499268, 2000.0], [1.455731894e-10, 2.590861083e-08, -1.0, 2000.0], [-0.999999875, -6.189255252e-11, -0.0004999995985, 2000.0], [0.8944271678, -0.44721332, -0.0005366216217, 2500.0], [0.8942481999, 1.233911471e-09, -0.4475713987, 2500.0], [0.4472140294, -0.894426813, -0.0005366778619, 2500.0], [0.447141854, -6.331739179e-08, -0.8944630581, 2500.0], [6.047983974e-10, -0.8942484278, -0.4475709434, 2500.0], [-1.547638207e-10, -0.4471420937, -0.8944629383, 2500.0], [6.038469206e-11, 0.4471424734, -0.8944627485, 2500.0], [-2.987575823e-10, 0.8942483962, -0.4475710065, 2500.0], [-0.4472142273, -0.8944267141, -0.0005366223904, 2500.0], [-0.4471422325, 2.979426711e-09, -0.894462869, 2500.0], [-0.8944272642, -0.4472131271, -0.0005366111842, 2500.0], [-0.8942481864, -1.203342597e-08, -0.4475714257, 2500.0], [0.8163150495, -0.4082259566, -0.4086334645, 3000.0], [0.8163149864, 0.4082255761, -0.4086339707, 3000.0], [0.4082262058, -0.816314944, -0.4086334263, 3000.0], [0.4081581457, -0.408157277, -0.816587145, 3000.0], [0.408157348, 0.4081578487, -0.8165872579, 3000.0], [0.4082253801, 0.8163154, -0.4086333403, 3000.0], [-0.4082260024, -0.8163148249, -0.4086338675, 3000.0], [-0.4081577425, -0.408157098, -0.816587436, 3000.0], [-0.4081578271, 0.4081579636, -0.816586961, 3000.0], [-0.4082254286, 0.8163152063, -0.4086336787, 3000.0], [-0.8163152896, -0.4082256582, -0.408633283, 3000.0], [-0.8163150614, 0.4082255313, -0.4086338657, 3000.0], [0.7071071135, -0.7071063605, -0.0003535496407, 4000.0], [0.7069299418, -5.319339341e-09, -0.7072835764, 4000.0], [-9.789377913e-11, -0.7069302433, -0.707283275, 4000.0], [1.567798364e-10, 0.7069298265, -0.7072836916, 4000.0], [-0.7071066491, -0.7071068248, -0.0003535998457, 4000.0], [-0.7069299747, 3.830753602e-08, -0.7072835434, 4000.0], [0.6665928365, -0.6665925637, -0.3336290519, 4500.0], [0.6664856674, -0.3333169916, -0.6668557852, 4500.0], [0.6664856527, 0.3333167604, -0.6668559155, 4500.0], [0.6665929437, 0.6665923207, -0.3336293233, 4500.0], [0.333317104, -0.6664855564, -0.66685584, 4500.0], [0.3333173941, 0.6664856233, -0.6668556281, 4500.0], [4.085725123e-11, -0.9999999012, -0.0004444170368, 4500.0], [1.455731894e-10, 2.590861083e-08, -1.0, 4500.0], [-0.3333166201, -0.6664858367, -0.6668558017, 4500.0], [-0.3333166057, 0.6664855235, -0.6668561219, 4500.0], [-0.6665924266, -0.666592734, -0.3336295307, 4500.0], [-0.6664858483, -0.3333171152, -0.6668555426, 4500.0], [-0.6664853425, 0.3333167888, -0.6668562113, 4500.0], [-0.6665924202, 0.666592617, -0.3336297773, 4500.0], [-0.9999999012, 3.742696584e-11, -0.0004444399636, 4500.0], [0.9486830278, -0.3162282667, -0.0004427363325, 5000.0], [0.9485630721, 2.321566786e-08, -0.3165882157, 5000.0], [0.3162277787, -0.9486831905, -0.0004427124981, 5000.0], [0.3162084303, -1.470391669e-08, -0.9486897431, 5000.0], [6.094271403e-11, -0.9485631972, -0.3165878406, 5000.0], [3.727802446e-10, -0.3160571874, -0.9487401406, 5000.0], [2.102303804e-10, 0.3162084941, -0.9486897218, 5000.0], [2.418275742e-10, 0.9485631902, -0.3165878617, 5000.0], [-0.3162281986, -0.9486830505, -0.0004427240341, 5000.0], [-0.3162086596, -2.213515469e-08, -0.9486896667, 5000.0], [-0.9486830937, -0.3162280692, -0.0004427716254, 5000.0], [-0.9485632352, -2.792397978e-09, -0.3165877268, 5000.0], [0.9044196305, -0.3014910643, -0.3018745932, 5500.0], [0.9044195348, 0.3014912943, -0.3018746504, 5500.0], [0.3014912367, -0.9044193748, -0.3018751873, 5500.0], [0.3015110819, -0.3013465199, -0.9045890462, 5500.0], [0.3014815607, 0.3014810386, -0.9045540625, 5500.0], [0.301491691, 0.9044192968, -0.3018749673, 5500.0], [-0.3014917901, -0.9044192099, -0.3018751286, 5500.0], [-0.3015110626, -0.3013465021, -0.9045890585, 5500.0], [-0.3014814747, 0.3014810781, -0.904554078, 5500.0], [-0.301491225, 0.904419444, -0.3018749917, 5500.0], [-0.9044195788, -0.3014910964, -0.301874716, 5500.0], [-0.9044196065, 0.3014912379, -0.3018744917, 5500.0], [0.5772539059, -0.577254112, -0.5775427416, 6000.0], [0.5772537687, 0.5772545673, -0.5775424235, 6000.0], [-0.5772541227, -0.5772538622, -0.5775427744, 6000.0], [-0.577254148, 0.5772543081, -0.5775423035, 6000.0], [0.8320501259, -0.5547003438, -0.0003413330173, 6500.0], [0.8319060448, 3.098869511e-08, -0.5549165096, 6500.0], [0.5546999144, -0.8320504122, -0.0003413904583, 6500.0], [0.554572481, -4.940954412e-08, -0.8321354236, 6500.0], [6.072960914e-10, -0.8319059468, -0.5549166565, 6500.0], [-3.666727552e-10, -0.5545724001, -0.8321354776, 6500.0], [2.11767819e-10, 0.5545717321, -0.8321359228, 6500.0], [-3.600334341e-10, 0.831906107, -0.5549164164, 6500.0], [-0.5546999789, -0.8320503692, -0.0003413141108, 6500.0], [-0.5545722601, 2.913643411e-08, -0.8321355709, 6500.0], [-0.832050099, -0.5547003842, -0.0003413181217, 6500.0], [-0.8319060534, 3.281216423e-10, -0.5549164967, 6500.0], [0.8017208664, -0.53446813, -0.2675583495, 7000.0], [0.8016418421, -0.2672396717, -0.5347460283, 7000.0], [0.8016418981, 0.2672394531, -0.5347460537, 7000.0], [0.8017207264, 0.534468159, -0.267558711, 7000.0], [0.5344681068, -0.8017208029, -0.2675585861, 7000.0], [0.53442475, -0.2671552934, -0.8018841786, 7000.0], [0.5343916032, 0.2672533946, -0.8018735795, 7000.0], [0.5344678393, 0.8017210021, -0.2675585238, 7000.0], [0.2672396447, -0.8016419395, -0.5347458958, 7000.0], [0.2672530582, -0.5343914545, -0.8018737907, 7000.0], [0.2672532447, 0.5343918496, -0.8018734652, 7000.0], [0.2672394535, 0.8016416949, -0.534746358, 7000.0], [-0.2672393738, -0.8016420235, -0.5347459053, 7000.0], [-0.2672529745, -0.5343914835, -0.8018737993, 7000.0], [-0.2672527998, 0.534391969, -0.801873534, 7000.0], [-0.2672395729, 0.8016417046, -0.5347462838, 7000.0], [-0.534468046, -0.8017208702, -0.2675585059, 7000.0], [-0.534424298, -0.2671553634, -0.8018844565, 7000.0], [-0.5343916999, 0.2672534444, -0.8018734985, 7000.0], [-0.5344680464, 0.801720919, -0.267558359, 7000.0], [-0.8017210357, -0.5344679886, -0.2675581246, 7000.0], [-0.8016417412, -0.2672397248, -0.5347461531, 7000.0], [-0.8016420535, 0.2672394791, -0.5347458078, 7000.0], [-0.8017211137, 0.5344675679, -0.2675587314, 7000.0], [2.651765635e-12, -0.9999999687, -0.0002500086681, 8000.0], [1.455731894e-10, 2.590861083e-08, -1.0, 8000.0], [-0.9999999687, -1.852948745e-11, -0.0002500002363, 8000.0]], 'mrtrix_version': '3.0.2'}}
dwibiascorrect: [DEBUG] path.name_temporary() (from image.py:33): /home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/mrtrix-tmp-6azLV9.json
dwibiascorrect: [DEBUG] run.exe_name() (from run.py:546): mrinfo -> mrinfo
dwibiascorrect: [DEBUG] run.version_match() (from image.py:34): Version-matched executable for mrinfo: /home/localadmin/Softwares/miniconda3/bin/mrinfo
dwibiascorrect: [DEBUG] run.exe_name() (from image.py:34): /home/localadmin/Softwares/miniconda3/bin/mrinfo -> /home/localadmin/Softwares/miniconda3/bin/mrinfo
dwibiascorrect: Loading header for image file 'mask.mif'
dwibiascorrect: [DEBUG] image.__init__() (from image.py:179): ['/home/localadmin/Softwares/miniconda3/bin/mrinfo', 'mask.mif', '-json_all', '/home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/mrtrix-tmp-6azLV9.json']
dwibiascorrect: [DEBUG] image.__init__() (from image.py:179): {'_name': 'mask.mif', '_size': [96, 96, 38], '_spacing': [2.20833, 2.20833, 3.0], '_strides': [1, 2, 3], '_format': 'MRtrix', '_datatype': 'Bit', '_intensity_offset': 0.0, '_intensity_scale': 1.0, '_transform': [[0.999999943880049, 5.33884719919637e-08, 0.000335022184972424, -102.900543212891], [1.57276657824971e-05, 0.998889975224889, -0.0471043187585057, -93.3131484985352], [-0.00033465286422834, 0.0471043245914531, 0.998889919317656, -23.3364963531494], [0.0, 0.0, 0.0, 1.0]], '_keyval': {'command_history': '/home/localadmin/Softwares/miniconda3/bin/mrconvert /home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/flirt_dwimask/dwi_brain_mask.nii.gz /home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/mask.mif -datatype bit -info  (version=3.0.2)', 'comments': 'FSL5.0', 'mrtrix_version': '3.0.2'}}
dwibiascorrect: [DEBUG] image.match() (from dwibiascorrect:69): 'in.mif' 'mask.mif' image match
dwibiascorrect: [DEBUG] run.exe_name() (from run.py:546): dwiextract -> dwiextract
dwibiascorrect: [DEBUG] run.version_match() (from run.py:330): Version-matched executable for dwiextract: /home/localadmin/Softwares/miniconda3/bin/dwiextract
dwibiascorrect: [DEBUG] run._shebang() (from run.py:340): File "/home/localadmin/Softwares/miniconda3/bin/dwiextract": Not a text file
dwibiascorrect: [DEBUG] run.exe_name() (from run.py:546): mrmath -> mrmath
dwibiascorrect: [DEBUG] run.version_match() (from run.py:330): Version-matched executable for mrmath: /home/localadmin/Softwares/miniconda3/bin/mrmath
dwibiascorrect: [DEBUG] run._shebang() (from run.py:340): File "/home/localadmin/Softwares/miniconda3/bin/mrmath": Not a text file
dwibiascorrect: [DEBUG] run.command() (from ants.py:64): To execute: [['/home/localadmin/Softwares/miniconda3/bin/dwiextract', 'in.mif', '-', '-bzero', '-info'], ['/home/localadmin/Softwares/miniconda3/bin/mrmath', '-', 'mean', 'mean_bzero.mif', '-axis', '3', '-info']]
Command:  dwiextract in.mif - -bzero | mrmath - mean mean_bzero.mif -axis 3
          dwiextract: [INFO] opening image "in.mif"...
          dwiextract: [INFO] image "in.mif" opened with dimensions 96x96x38x129, voxel spacing 2.2083300000000001x2.2083300000000001x3x5.9000000000000004, datatype Float32LE
          dwiextract: [INFO] found 129x4 diffusion gradient table
          dwiextract: [INFO] creating image "-"...
          dwiextract: [INFO] image "/home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/mrtrix-tmp-sK5XHm.mif" created with dimensions 96x96x38x1, voxel spacing 2.2083300000000001x2.2083300000000001x3x5.9000000000000004, datatype Float32LE
          dwiextract: [100%] extracting volumes
          mrmath: [INFO] opening image "-"...
          mrmath: [INFO] image "/home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/mrtrix-tmp-sK5XHm.mif" opened with dimensions 96x96x38x1, voxel spacing 2.2083300000000001x2.2083300000000001x3x5.9000000000000004, datatype Float32LE
          mrmath: [INFO] creating image "mean_bzero.mif"...
          mrmath: [INFO] image "mean_bzero.mif" created with dimensions 96x96x38, voxel spacing 2.2083300000000001x2.2083300000000001x3, datatype Float32LE
          mrmath: [100%] computing mean along axis 3...
dwibiascorrect: [DEBUG] run.exe_name() (from run.py:546): mrconvert -> mrconvert
dwibiascorrect: [DEBUG] run.version_match() (from run.py:330): Version-matched executable for mrconvert: /home/localadmin/Softwares/miniconda3/bin/mrconvert
dwibiascorrect: [DEBUG] run._shebang() (from run.py:340): File "/home/localadmin/Softwares/miniconda3/bin/mrconvert": Not a text file
dwibiascorrect: [DEBUG] run.command() (from ants.py:68): To execute: [['/home/localadmin/Softwares/miniconda3/bin/mrconvert', 'mean_bzero.mif', 'mean_bzero.nii', '-strides', '+1,+2,+3', '-info']]
Command:  mrconvert mean_bzero.mif mean_bzero.nii -strides +1,+2,+3
          mrconvert: [INFO] opening image "mean_bzero.mif"...
          mrconvert: [INFO] image "mean_bzero.mif" opened with dimensions 96x96x38, voxel spacing 2.2083300000000001x2.2083300000000001x3, datatype Float32LE
          mrconvert: [INFO] no valid diffusion gradient table found
          mrconvert: [INFO] error importing diffusion gradient table for image "mean_bzero.mif"
          mrconvert: [INFO] opening image "+1,+2,+3"...
          mrconvert: [INFO] creating image "mean_bzero.nii"...
          mrconvert: [INFO] image "mean_bzero.nii" created with dimensions 96x96x38, voxel spacing 2.2083300000000001x2.2083300000000001x3, datatype Float32LE
          mrconvert: [100%] copying from "mean_bzero.mif" to "mean_bzero.nii"
dwibiascorrect: [DEBUG] run.exe_name() (from run.py:546): mrconvert -> mrconvert
dwibiascorrect: [DEBUG] run.version_match() (from run.py:330): Version-matched executable for mrconvert: /home/localadmin/Softwares/miniconda3/bin/mrconvert
dwibiascorrect: [DEBUG] run._shebang() (from run.py:340): File "/home/localadmin/Softwares/miniconda3/bin/mrconvert": Not a text file
dwibiascorrect: [DEBUG] run.command() (from ants.py:69): To execute: [['/home/localadmin/Softwares/miniconda3/bin/mrconvert', 'mask.mif', 'mask.nii', '-strides', '+1,+2,+3', '-info']]
Command:  mrconvert mask.mif mask.nii -strides +1,+2,+3
          mrconvert: [INFO] opening image "mask.mif"...
          mrconvert: [INFO] image "mask.mif" opened with dimensions 96x96x38, voxel spacing 2.2083300000000001x2.2083300000000001x3, datatype Bit
          mrconvert: [INFO] no valid diffusion gradient table found
          mrconvert: [INFO] error importing diffusion gradient table for image "mask.mif"
          mrconvert: [INFO] opening image "+1,+2,+3"...
          mrconvert: [INFO] creating image "mask.nii"...
          mrconvert: [WARNING] requested datatype (Bit) not supported - substituting with UInt8
          mrconvert: [INFO] image "mask.nii" created with dimensions 96x96x38, voxel spacing 2.2083300000000001x2.2083300000000001x3, datatype UInt8
          mrconvert: [100%] copying from "mask.mif" to "mask.nii"
dwibiascorrect: [DEBUG] run.exe_name() (from run.py:546): N4BiasFieldCorrection -> N4BiasFieldCorrection
dwibiascorrect: [DEBUG] run.version_match() (from run.py:330): Version-matched executable for N4BiasFieldCorrection: /home/localadmin/Softwares/miniconda3/bin/N4BiasFieldCorrection
dwibiascorrect: [DEBUG] run._shebang() (from run.py:340): File "/home/localadmin/Softwares/miniconda3/bin/N4BiasFieldCorrection": Not a text file
dwibiascorrect: [DEBUG] run.command() (from ants.py:72): To execute: [['/home/localadmin/Softwares/miniconda3/bin/N4BiasFieldCorrection', '-d', '3', '-i', 'mean_bzero.nii', '-w', 'mask.nii', '-o', '[corrected.nii,init_bias.nii]', '-s', '4', '-b', '[100,3]', '-c', '[1000,0.0]', '-info']]
Command:  N4BiasFieldCorrection -d 3 -i mean_bzero.nii -w mask.nii -o [corrected.nii,init_bias.nii] -s 4 -b [100,3] -c [1000,0.0]
          ERROR:  Invalid command line flags found! Aborting execution.

dwibiascorrect: [ERROR] N4BiasFieldCorrection -d 3 -i mean_bzero.nii -w mask.nii -o [corrected.nii,init_bias.nii] -s 4 -b [100,3] -c [1000,0.0] (ants.py:72)
dwibiascorrect: [ERROR] Information from failed command:
dwibiascorrect:
                ERROR:  Invalid flag provided in
                ERROR:  Invalid command line flags found! Aborting execution.
dwibiascorrect:
dwibiascorrect: [ERROR] For debugging, inspect contents of scratch directory: /home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/
dwibiascorrect: Scratch directory retained; location: /home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-XEGOZD/

Looking at the line:

dwibiascorrect: [DEBUG] run.command() (from ants.py:72): To execute: [['/home/localadmin/Softwares/miniconda3/bin/N4BiasFieldCorrection', '-d', '3', '-i', 'mean_bzero.nii', '-w', 'mask.nii', '-o', '[corrected.nii,init_bias.nii]', '-s', '4', '-b', '[100,3]', '-c', '[1000,0.0]', '-info']]

It seems an extra option flag -info is added to the N4BiasFieldCorrection.

Running dwibiascorrect without the flag -debug succeeds, see below.

Command:

/home/localadmin/Softwares/miniconda3/bin/dwibiascorrect ants -mask /home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/flirt_dwimask/dwi_brain_mask.nii.gz -bias diffusion_denoised_biasfield.mif -force /home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/dwi_denoise/diffusion_denoised.mif /home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/dwi_biascorrect/diffusion_denoised_biascorr.mif
dwibiascorrect: 
dwibiascorrect: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the help page (-help option) for more information.
dwibiascorrect: 
dwibiascorrect: [WARNING] Output file 'diffusion_denoised_biasfield.mif' already exists; will be overwritten at script completion
dwibiascorrect: Generated scratch directory: /home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-683WFE/
Command:  mrconvert /home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/dwi_denoise/diffusion_denoised.mif /home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-683WFE/in.mif
Command:  mrconvert /home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/flirt_dwimask/dwi_brain_mask.nii.gz /home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-683WFE/mask.mif -datatype bit
dwibiascorrect: Changing to scratch directory (/home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-683WFE/)
Command:  dwiextract in.mif - -bzero | mrmath - mean mean_bzero.mif -axis 3
Command:  mrconvert mean_bzero.mif mean_bzero.nii -strides +1,+2,+3
Command:  mrconvert mask.mif mask.nii -strides +1,+2,+3
Command:  N4BiasFieldCorrection -d 3 -i mean_bzero.nii -w mask.nii -o [corrected.nii,init_bias.nii] -s 4 -b [100,3] -c [1000,0.0]
Command:  mrcalc mean_bzero.mif mask.mif -mult - | mrmath - sum - -axis 0 | mrmath - sum - -axis 1 | mrmath - sum - -axis 2 | mrdump -
Command:  mrcalc corrected.nii mask.mif -mult - | mrmath - sum - -axis 0 | mrmath - sum - -axis 1 | mrmath - sum - -axis 2 | mrdump -
Command:  mrcalc init_bias.nii 0.9515317417482443 -mult bias.mif
Command:  mrcalc in.mif bias.mif -div result.mif
Command:  mrconvert result.mif /home/localadmin/Desktop/HagmannTest/BIDS_out/ds-DSI/derivatives/nipype/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/dwi_biascorrect/diffusion_denoised_biascorr.mif
Command:  mrconvert bias.mif /home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/diffusion_denoised_biasfield.mif
dwibiascorrect: Changing back to original directory (/home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88)
dwibiascorrect: Deleting scratch directory (/home/localadmin/.local/share/Trash/files/dwibiascorrect-tmp-I6CQ88/dwibiascorrect-tmp-683WFE/)

Platform/Environment/Version

Please provide the following information:

• OS:
  Distributor ID: Ubuntu
  Description: Ubuntu 16.04.6 LTS
  Release: 16.04
  Codename: xenial

• MRtrix3 version:
  == mrinfo 3.0.2 ==
  64 bit release version, built Sep 30 2020, using Eigen 3.3.7
  Author(s): J-Donald Tournier (d.tournier@brain.org.au) and Robert E. Smith (robert.smith@florey.edu.au)
  Copyright (c) 2008-2020 the MRtrix3 contributors.

---

[Lestropie]

Hi Sebastien,

Thanks for the report; it looks like I'm going to have to re-think exactly how this functionality should work.

For reference, the additional -info flag is inserted here. The "N4BiasFieldCorrection" binary is being erroneously classified as an MRtrix3 executable, because it resides in the same location as where the MRtrix3 binaries are expected to reside relative to the Python API (code). In your case, the location of this binary is "/home/localadmin/Softwares/miniconda3/bin/N4BiasFieldCorrection". So I'm assuming that Anaconda is installing multiple softwares into the same bin/ directory, in which case my logic for classifying MRtrix3 v.s. non-MRtrix3 binaries does not work.

---

As far as how I might go about resolving it:

1. Disable that functionality entirely (but this would result in a loss of capability of the -debug flag for Python scripts);
2. Bake a list of MRtrix3 executables into lib/mrtrix3/, perhaps that gets generated by the build script and verified in CI;
3. Do an execution test, e.g. by invoking "<cmdname> __print_full_usage__"; would potentially slow down any script that involves many executions of fast commands, though I suppose at least in the case of running the same command repeatedly, a dictionary could be constructed at runtime so that each unique command need only be tested once per script execution.

[jdtournier]

Could also use an environment variable (e.g. MRTRIX_LOGLEVEL) instead of a command-line option...? Might be useful anyway...

[Lestropie]

Yep, that's an attractive 4. option.

[sebastientourbier]

Thanks a lot Robert and Jacques-Donald !

[Lestropie]

Closing issue and deferring to PR #2316, which implements @jdtournier's proposed solution above.