Hi Donald,
I hope I did it right:
- The Command
dwifslpreproc B_04*.mif B_05_DWI_01.mif -pe_dir AP -rpe_pair -se_epi G_01_*.mif -eddy_options "--data_is_shelled --slm=linear" -debug -nocleanup
- The full Output:
miracum@DIZ-UMMD-B175:/$ dwifslpreproc B_04*.mif B_05_DWI_01.mif -pe_dir AP -rpe_pair -se_epi G_01_*.mif -eddy_options "--data_is_shelled --slm=linear" -debug -nocleanup
dwifslpreproc:
dwifslpreproc: 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.
dwifslpreproc:
dwifslpreproc: [DEBUG] path.from_user() (from dwifslpreproc:92): B_04_denoised_withoutFirstB0_AP_wk92_1.8mm_3172_2019.mif -> /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/B_04_denoised_withoutFirstB0_AP_wk92_1.8mm_3172_2019.mif
dwifslpreproc: [DEBUG] path.name_temporary() (from image.py:33): /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/mrtrix-tmp-CMnN0q.json
dwifslpreproc: [DEBUG] run.exe_name() (from run.py:546): mrinfo -> mrinfo
dwifslpreproc: [DEBUG] run.version_match() (from image.py:34): Version-matched executable for mrinfo: /home/miracum/mrtrix3/bin/mrinfo
dwifslpreproc: [DEBUG] run.exe_name() (from image.py:34): /home/miracum/mrtrix3/bin/mrinfo -> /home/miracum/mrtrix3/bin/mrinfo
dwifslpreproc: Loading header for image file '/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/B_04_denoised_withoutFirstB0_AP_wk92_1.8mm_3172_2019.mif'
dwifslpreproc: [DEBUG] image.__init__() (from image.py:134): ['/home/miracum/mrtrix3/bin/mrinfo', '/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/B_04_denoised_withoutFirstB0_AP_wk92_1.8mm_3172_2019.mif', '-json_all', '/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/mrtrix-tmp-CMnN0q.json']
dwifslpreproc: [DEBUG] image.__init__() (from image.py:134): {'_intensity_offset': 0.0, '_format': u'MRtrix', '_transform': [[1.0, 0.0, 0.0, -104.76000893116], [0.0, 0.9988061374039, -0.0488497685184, -74.3036471873993], [-0.0, 0.0488497685184, 0.9988061374039, -86.3906509626887], [0.0, 0.0, 0.0, 1.0]], '_intensity_scale': 1.0, '_datatype': u'Float32LE', '_name': u'/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/B_04_denoised_withoutFirstB0_AP_wk92_1.8mm_3172_2019.mif', '_keyval': {u'EchoTime': 0.0664, u'RepetitionTime': 3.98, u'mrtrix_version': u'3.0.2-31-g67bf6093', u'FlipAngle': [90, 180], u'PartialFourier': 0.875, u'comments': [u'wk92_3201 (wk92_3201) [MR] DTIcmrr_1.8iso_3shell_b2400_TE66_SMS2_AP', u'study: baecke^Test [ ORIGINAL PRIMARY DIFFUSION NONE MB ND NORM MOSAIC ]', u'DOB: 01/01/1960', u'DOS: 02/04/2019 15:00:11'], u'PhaseEncodingDirection': u'j-', u'MultibandAccelerationFactor': 2, u'SliceEncodingDirection': u'k', u'SliceTiming': [0.0, 1.88, 3.76, 1.6825, 3.5625, 1.485, 3.365, 1.285, 3.1675, 1.0875, 2.9675, 0.89, 2.77, 0.6925, 2.5725, 0.495, 2.375, 0.295, 2.1775, 0.0975, 1.98, 3.86, 1.78, 3.6625, 1.5825, 3.4625, 1.385, 3.265, 1.1875, 3.0675, 0.99, 2.87, 0.79, 2.6725, 0.5925, 2.4725, 0.395, 2.275, 0.1975, 2.0775, 0.0, 1.88, 3.76, 1.6825, 3.5625, 1.485, 3.365, 1.285, 3.1675, 1.0875, 2.9675, 0.89, 2.77, 0.6925, 2.5725, 0.495, 2.375, 0.295, 2.1775, 0.0975, 1.98, 3.86, 1.78, 3.6625, 1.5825, 3.4625, 1.385, 3.265, 1.1875, 3.0675, 0.99, 2.87, 0.79, 2.6725, 0.5925, 2.4725, 0.395, 2.275, 0.1975, 2.0775], u'TotalReadoutTime': 0.0339, u'command_history': [u'mrconvert series_6_DTIcmrr_1.8iso_3shell_b2400_TE66_SMS2_AP/ Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/B_01_DWI_wk92_1.8mm_3172_2019.mif (version=3.0.2-31-g67bf6093)', u'dwidenoise B_01_DWI_wk92_1.8mm_3172_2019.mif B_02_denoised_wk92_1.8mm_3172_2019.mif (version=3.0.2-31-g67bf6093)', u'mrdegibbs B_02_denoised_wk92_1.8mm_3172_2019.mif B_03_denoised_dering_wk92_1.8mm_3172_2019.mif (version=3.0.2-31-g67bf6093)', u"mrconvert B_03_denoised_dering_wk92_1.8mm_3172_2019.mif -coord 3 '1:131' B_04_denoised_withoutFirstB0_AP_wk92_1.8mm_3172_2019.mif (version=3.0.2-31-g67bf6093)"], u'dw_scheme': [[0.57735026, -0.57735038, 0.57735032, 5.0], [-0.93799639, 0.18036179, -0.29602784, 265.0], [-0.25487185, -0.966968, 0.00361619, 265.0], [0.26850852, 0.00834691, -0.96324116, 265.0], [-0.51920122, 0.79041028, 0.32508722, 270.0], [0.60796934, 0.48912075, 0.62540734, 270.0], [0.06567493, -0.67067617, 0.738837, 270.0], [0.87254018, 0.23766665, -0.426835, 265.0], [-0.04770676, 0.61473256, 0.78729141, 270.0], [-0.61817431, 0.64060622, -0.45550442, 265.0], [0.57735026, -0.57735038, 0.57735032, 5.0], [-0.00844199, 0.41697538, -0.90887851, 795.0], [-0.00954073, -0.91078699, -0.41276625, 800.0], [0.99899274, 0.01754255, -0.04130214, 800.0], [0.59608793, -0.75320059, 0.27815136, 800.0], [-0.55697346, -0.35443673, -0.75110275, 795.0], [0.62954617, -0.1537956, -0.76158941, 795.0], [0.5848856, 0.79228795, -0.17374842, 800.0], [-0.69784927, 0.26691502, -0.66465235, 795.0], [0.57201278, -0.68423903, -0.45234761, 795.0], [-0.08775683, -0.89342618, 0.44055453, 805.0], [0.03069417, -0.31166795, -0.94969517, 795.0], [0.75991088, 0.37810048, -0.52874893, 795.0], [-0.81626874, -0.49694982, -0.29452717, 800.0], [-0.87618738, 0.47683981, 0.07013749, 800.0], [-0.16620705, 0.98595381, -0.01645165, 800.0], [-0.29868853, 0.0554062, -0.95274091, 795.0], [-0.45341623, -0.79873651, -0.39551723, 800.0], [0.57735026, -0.57735038, 0.57735032, 5.0], [-0.42452773, -0.37482208, 0.8241871, 805.0], [-0.9209404, 0.00791028, -0.38962328, 800.0], [0.22224967, -0.62930661, -0.74470007, 795.0], [-0.26975873, 0.70844209, -0.65218097, 795.0], [-0.88675982, 0.1464432, 0.43841934, 805.0], [-0.86522663, -0.48307237, 0.13425334, 800.0], [-0.23591673, -0.62432283, -0.7446909, 795.0], [-0.38000572, -0.71244895, 0.58992553, 805.0], [0.54081929, -0.83548737, -0.09734078, 800.0], [0.19028635, 0.04629009, -0.98063672, 795.0], [0.8403576, -0.41960761, 0.34311581, 800.0], [-0.26245797, -0.96274799, -0.06505373, 800.0], [0.41725472, -0.40053666, 0.81576282, 805.0], [0.50897622, -0.43284231, -0.74403679, 795.0], [0.77680987, 0.2021421, 0.59640986, 805.0], [0.25485501, -0.90353632, 0.34448692, 805.0], [-0.91732264, -0.16325313, 0.36313558, 800.0], [0.57735026, -0.57735038, 0.57735032, 5.0], [-0.7151261, -0.6389727, -0.28338772, 2395.0], [0.69953507, -0.64524394, -0.30710104, 2395.0], [0.20471382, -0.46842951, 0.85945678, 2410.0], [-0.70392483, -0.26718506, 0.6581049, 2405.0], [0.07683749, 0.52291548, 0.84891433, 2410.0], [-0.03691429, 0.98218513, -0.18425412, 2395.0], [0.87106407, -0.1694538, 0.46101281, 2405.0], [-0.41322556, 0.18808559, 0.890993, 2410.0], [0.53669292, 0.78219616, -0.31643304, 2395.0], [-0.98549527, 0.09847239, 0.138211, 2400.0], [-0.5067274, -0.10754216, -0.85537255, 2390.0], [-0.14192897, 0.91690445, 0.37301761, 2405.0], [-0.54972976, 0.72419852, -0.41633335, 2395.0], [0.57735026, -0.57735038, 0.57735032, 5.0], [0.27551633, 0.55964226, -0.78159529, 2390.0], [0.92677081, 0.3741481, -0.03330019, 2400.0], [-0.32523698, -0.80635041, -0.49398375, 2395.0], [-0.74979568, 0.3021363, 0.58865958, 2405.0], [-0.0381232, 0.02387862, -0.99898756, 2390.0], [-0.82192928, 0.5536052, -0.13399068, 2400.0], [-0.78196025, -0.29278985, -0.55028361, 2395.0], [0.04695667, -0.82578087, 0.56203294, 2405.0], [0.34363219, -0.65634263, -0.67166305, 2395.0], [0.36694175, 0.92868835, 0.05377373, 2400.0], [0.58779222, -0.35824448, 0.72536969, 2410.0], [0.44590971, -0.89479852, -0.02235875, 2400.0], [-0.80228531, -0.45777029, 0.38312486, 2405.0], [0.57735026, -0.57735038, 0.57735032, 5.0], [0.34082696, 0.19555956, -0.91956145, 2390.0], [0.45827392, 0.50191772, 0.73352814, 2410.0], [0.9766016, 0.07120875, 0.20292567, 2400.0], [-0.87912923, 0.00278722, 0.47657546, 2405.0], [0.26533911, 0.84508491, -0.46414116, 2395.0], [-0.13273431, 0.32269147, 0.93715096, 2410.0], [-0.04817256, -0.98719782, -0.15205145, 2400.0], [-0.88953441, 0.42274547, 0.17324825, 2400.0], [0.35044891, -0.17674224, 0.91975427, 2410.0], [-0.71226263, -0.7013545, 0.02799733, 2400.0], [-0.34622052, 0.69174242, -0.6337378, 2395.0], [-0.00798193, 0.76848978, 0.63981217, 2405.0], [0.77544743, -0.45740286, 0.43527442, 2405.0], [0.57735026, -0.57735038, 0.57735032, 5.0], [-0.54308504, -0.54693681, 0.63711745, 2405.0], [-0.45480615, 0.79940784, 0.39255375, 2405.0], [0.73616558, 0.02087326, 0.67647952, 2405.0], [-0.63462621, 0.03127369, 0.77218628, 2410.0], [0.32392678, -0.90786749, 0.26617318, 2405.0], [-0.88059115, -0.38648558, -0.27420464, 2395.0], [-0.2354628, -0.25322038, -0.93831575, 2390.0], [0.07630058, 0.3675378, -0.92687345, 2390.0], [0.55874109, -0.47803265, -0.67771161, 2395.0], [-0.48846912, -0.82825184, -0.27458453, 2395.0], [0.95687282, -0.25682393, 0.13577951, 2400.0], [-0.94116914, -0.19944602, 0.27280381, 2405.0], [0.65967035, -0.75093919, 0.03041869, 2400.0], [0.57735026, -0.57735038, 0.57735032, 5.0], [-0.25278005, -0.94532871, 0.20604758, 2405.0], [-0.60051364, -0.58556086, -0.54452008, 2395.0], [-0.01499894, -0.65237659, 0.7577464, 2410.0], [0.20465028, -0.05136202, -0.97748685, 2390.0], [-0.21907493, 0.96953458, 0.10958306, 2400.0], [0.88642716, -0.27435794, -0.37279308, 2395.0], [0.24154605, 0.67337972, 0.69872403, 2405.0], [0.7273013, 0.63382012, -0.26325819, 2395.0], [-0.59000188, 0.14625072, -0.79404575, 2390.0], [-0.51236099, -0.32176894, 0.79621017, 2410.0], [0.28353515, -0.49025899, -0.82416838, 2390.0], [0.56522822, -0.56330436, 0.60266501, 2405.0], [-0.89909619, -0.10859653, -0.42406702, 2395.0], [0.57735026, -0.57735038, 0.57735032, 5.0], [0.14862876, 0.91822112, 0.36712319, 2405.0], [0.22601262, -0.86431515, 0.44930792, 2405.0], [-0.67151958, 0.55000257, 0.49654663, 2405.0], [-0.98989004, -0.13933425, 0.02652614, 2400.0], [-0.42540705, -0.7169807, 0.55223876, 2405.0], [-0.5908553, -0.29913455, -0.74927193, 2390.0], [0.12369111, -0.24178907, 0.96241289, 2410.0], [0.67555416, -0.69531924, 0.24527054, 2405.0], [0.5389896, 0.84085304, -0.04956008, 2400.0], [-0.24661002, 0.80427885, 0.54066509, 2405.0], [-0.7700237, -0.06002368, 0.63518566, 2405.0], [-0.83604592, -0.54135126, -0.08925267, 2400.0], [-0.26947674, -0.0553134, -0.96141708, 2390.0], [0.57735026, -0.57735038, 0.57735032, 5.0]], u'PixelBandwidth': 2085, u'DiffusionScheme': u'Monopolar'}, '_size': [120, 120, 80, 131], '_spacing': [1.8, 1.8, 1.8, None], '_strides': [-1, -2, 3, 4]}
dwifslpreproc: [DEBUG] image.check_3d_nonunity() (from dwifslpreproc:92): Image '/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/B_04_denoised_withoutFirstB0_AP_wk92_1.8mm_3172_2019.mif' is >= 3D, and does not contain a unity spatial dimension
dwifslpreproc: [DEBUG] fsl.exe_name() (from dwifslpreproc:119): topup
dwifslpreproc: [DEBUG] fsl.exe_name() (from dwifslpreproc:120): applytopup
dwifslpreproc: [DEBUG] fsl.eddy_binary() (from dwifslpreproc:122): CUDA version 9.1: eddy_cuda9.1
dwifslpreproc: [DEBUG] fsl.suffix() (from dwifslpreproc:124): NIFTI_GZ -> .nii.gz
dwifslpreproc: Generated scratch directory: /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/
dwifslpreproc: [DEBUG] path.to_scratch() (from dwifslpreproc:181): dwi.json -> /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/dwi.json
dwifslpreproc: [DEBUG] path.from_user() (from dwifslpreproc:182): B_04_denoised_withoutFirstB0_AP_wk92_1.8mm_3172_2019.mif -> /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/B_04_denoised_withoutFirstB0_AP_wk92_1.8mm_3172_2019.mif
dwifslpreproc: [DEBUG] path.to_scratch() (from dwifslpreproc:182): dwi.mif -> /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/dwi.mif
dwifslpreproc: [DEBUG] run.exe_name() (from run.py:546): mrconvert -> mrconvert
dwifslpreproc: [DEBUG] run.version_match() (from run.py:330): Version-matched executable for mrconvert: /home/miracum/mrtrix3/bin/mrconvert
dwifslpreproc: [DEBUG] run._shebang() (from run.py:340): File "/home/miracum/mrtrix3/bin/mrconvert": Not a text file
dwifslpreproc: [DEBUG] run.command() (from dwifslpreproc:182): To execute: [['/home/miracum/mrtrix3/bin/mrconvert', '/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/B_04_denoised_withoutFirstB0_AP_wk92_1.8mm_3172_2019.mif', '/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/dwi.mif', '-json_export', '/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/dwi.json', '-info']]
Command: mrconvert /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/B_04_denoised_withoutFirstB0_AP_wk92_1.8mm_3172_2019.mif /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/dwi.mif -json_export /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/dwi.json
mrconvert: [INFO] opening image "/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/B_04_denoised_withoutFirstB0_AP_wk92_1.8mm_3172_2019.mif"...
mrconvert: [INFO] image "/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/B_04_denoised_withoutFirstB0_AP_wk92_1.8mm_3172_2019.mif" opened with dimensions 120x120x80x131, voxel spacing 1.8x1.8x1.8xnan, datatype Float32LE
mrconvert: [INFO] found 131x4 diffusion gradient table
mrconvert: [INFO] creating image "/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/dwi.mif"...
mrconvert: [INFO] image "/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/dwi.mif" created with dimensions 120x120x80x131, voxel spacing 1.8x1.8x1.8xnan, datatype Float32LE
mrconvert: [100%] copying from "/mnt/DATEN...AP_wk92_1.8mm_3172_2019.mif" to "/mnt/DATEN...lpreproc-tmp-WPH4E7/dwi.mif"
dwifslpreproc: [DEBUG] path.from_user() (from dwifslpreproc:184): G_01_B0_AP_PA_wk92_1.8mm_3172_2019.mif -> /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/G_01_B0_AP_PA_wk92_1.8mm_3172_2019.mif
dwifslpreproc: [DEBUG] path.name_temporary() (from image.py:33): /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/mrtrix-tmp-0Pv0lk.json
dwifslpreproc: [DEBUG] run.exe_name() (from run.py:546): mrinfo -> mrinfo
dwifslpreproc: [DEBUG] run.version_match() (from image.py:34): Version-matched executable for mrinfo: /home/miracum/mrtrix3/bin/mrinfo
dwifslpreproc: [DEBUG] run.exe_name() (from image.py:34): /home/miracum/mrtrix3/bin/mrinfo -> /home/miracum/mrtrix3/bin/mrinfo
dwifslpreproc: Loading header for image file '/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/G_01_B0_AP_PA_wk92_1.8mm_3172_2019.mif'
dwifslpreproc: [DEBUG] image.__init__() (from image.py:134): ['/home/miracum/mrtrix3/bin/mrinfo', '/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/G_01_B0_AP_PA_wk92_1.8mm_3172_2019.mif', '-json_all', '/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/mrtrix-tmp-0Pv0lk.json']
dwifslpreproc: [DEBUG] image.__init__() (from image.py:134): {'_intensity_offset': 0.0, '_format': u'MRtrix', '_transform': [[1.0, 0.0, 0.0, -104.76000893116], [0.0, 0.9988061374039, -0.0488497685184, -74.3036471873993], [-0.0, 0.0488497685184, 0.9988061374039, -86.3906509626887], [0.0, 0.0, 0.0, 1.0]], '_intensity_scale': 1.0, '_datatype': u'Float32LE', '_name': u'/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/G_01_B0_AP_PA_wk92_1.8mm_3172_2019.mif', '_keyval': {u'EchoTime': 0.0664, u'RepetitionTime': 3.98, u'mrtrix_version': u'3.0.2-31-g67bf6093', u'FlipAngle': [90, 180], u'PartialFourier': 0.875, u'comments': [u'wk92_3201 (wk92_3201) [MR] DTIcmrr_1.8iso_3shell_b2400_TE66_SMS2_AP', u'study: baecke^Test [ ORIGINAL PRIMARY DIFFUSION NONE MB ND NORM MOSAIC ]', u'DOB: 01/01/1960', u'DOS: 02/04/2019 15:00:11', u'wk92_3201 (wk92_3201) [MR] DTIcmrr_1.8iso_3shell_b2400_TE66_SMS2_PA', u'study: baecke^Test [ ORIGINAL PRIMARY M MB ND NORM ]', u'DOS: 02/04/2019 15:10:14'], u'MultibandAccelerationFactor': 2, u'SliceEncodingDirection': u'k', u'SliceTiming': [0.0, 1.88, 3.76250005, 1.6825, 3.5625, 1.48500001, 3.36500001, 1.28750002, 3.16750002, 1.09000003, 2.97000003, 0.889999986, 2.77250004, 0.692499995, 2.57249999, 0.495000005, 2.375, 0.297500014, 2.17750001, 0.100000001, 1.98000002, 3.8599999, 1.78250003, 3.6624999, 1.58500004, 3.46499991, 1.38499999, 3.26749992, 1.1875, 3.06750011, 0.99000001, 2.86999989, 0.792500019, 2.6724999, 0.595000029, 2.4749999, 0.395000011, 2.27749991, 0.197500005, 2.07999992, 0.0, 1.88, 3.76250005, 1.6825, 3.5625, 1.48500001, 3.36500001, 1.28750002, 3.16750002, 1.09000003, 2.97000003, 0.889999986, 2.77250004, 0.692499995, 2.57249999, 0.495000005, 2.375, 0.297500014, 2.17750001, 0.100000001, 1.98000002, 3.8599999, 1.78250003, 3.6624999, 1.58500004, 3.46499991, 1.38499999, 3.26749992, 1.1875, 3.06750011, 0.99000001, 2.86999989, 0.792500019, 2.6724999, 0.595000029, 2.4749999, 0.395000011, 2.27749991, 0.197500005, 2.07999992], u'pe_scheme': [[0.0, -1.0, 0.0, 0.0339], [0.0, 1.0, 0.0, 0.0339]], u'command_history': [u'variable', u'mrcat F_01_B0_AP_only_wk92_1.8mm_3172_2019.mif C_04_denoised_PA_OnlyB0_wk92_1.8mm_3172_2019.mif G_01_B0_AP_PA_wk92_1.8mm_3172_2019.mif -axis 3 (version=3.0.2-31-g67bf6093)'], u'PixelBandwidth': 2085, u'DiffusionScheme': u'Monopolar'}, '_size': [120, 120, 80, 2], '_spacing': [1.8, 1.8, 1.8, None], '_strides': [-1, -3, 4, 2]}
dwifslpreproc: [DEBUG] image.check_3d_nonunity() (from dwifslpreproc:184): Image '/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/G_01_B0_AP_PA_wk92_1.8mm_3172_2019.mif' is >= 3D, and does not contain a unity spatial dimension
dwifslpreproc: [DEBUG] path.from_user() (from dwifslpreproc:185): G_01_B0_AP_PA_wk92_1.8mm_3172_2019.mif -> /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/G_01_B0_AP_PA_wk92_1.8mm_3172_2019.mif
dwifslpreproc: [DEBUG] path.to_scratch() (from dwifslpreproc:185): se_epi.mif -> /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/se_epi.mif
dwifslpreproc: [DEBUG] run.exe_name() (from run.py:546): mrconvert -> mrconvert
dwifslpreproc: [DEBUG] run.version_match() (from run.py:330): Version-matched executable for mrconvert: /home/miracum/mrtrix3/bin/mrconvert
dwifslpreproc: [DEBUG] run._shebang() (from run.py:340): File "/home/miracum/mrtrix3/bin/mrconvert": Not a text file
dwifslpreproc: [DEBUG] run.command() (from dwifslpreproc:185): To execute: [['/home/miracum/mrtrix3/bin/mrconvert', '/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/G_01_B0_AP_PA_wk92_1.8mm_3172_2019.mif', '/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/se_epi.mif', '-info']]
Command: mrconvert /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/G_01_B0_AP_PA_wk92_1.8mm_3172_2019.mif /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/se_epi.mif
mrconvert: [INFO] opening image "/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/G_01_B0_AP_PA_wk92_1.8mm_3172_2019.mif"...
mrconvert: [INFO] image "/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/G_01_B0_AP_PA_wk92_1.8mm_3172_2019.mif" opened with dimensions 120x120x80x2, voxel spacing 1.8x1.8x1.8xnan, datatype Float32LE
mrconvert: [INFO] no valid diffusion gradient table found
mrconvert: [INFO] error importing diffusion gradient table for image "/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/G_01_B0_AP_PA_wk92_1.8mm_3172_2019.mif"
mrconvert: [INFO] creating image "/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/se_epi.mif"...
mrconvert: [INFO] image "/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/se_epi.mif" created with dimensions 120x120x80x2, voxel spacing 1.8x1.8x1.8xnan, datatype Float32LE
mrconvert: [100%] copying from "/mnt/DATEN...PA_wk92_1.8mm_3172_2019.mif" to "/mnt/DATEN...eproc-tmp-WPH4E7/se_epi.mif"
dwifslpreproc: Changing to scratch directory (/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/)
dwifslpreproc: [DEBUG] path.name_temporary() (from image.py:33): /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/mrtrix-tmp-f70Ask.json
dwifslpreproc: [DEBUG] run.exe_name() (from run.py:546): mrinfo -> mrinfo
dwifslpreproc: [DEBUG] run.version_match() (from image.py:34): Version-matched executable for mrinfo: /home/miracum/mrtrix3/bin/mrinfo
dwifslpreproc: [DEBUG] run.exe_name() (from image.py:34): /home/miracum/mrtrix3/bin/mrinfo -> /home/miracum/mrtrix3/bin/mrinfo
dwifslpreproc: Loading header for image file 'dwi.mif'
dwifslpreproc: [DEBUG] image.__init__() (from dwifslpreproc:193): ['/home/miracum/mrtrix3/bin/mrinfo', 'dwi.mif', '-json_all', '/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/mrtrix-tmp-f70Ask.json']
dwifslpreproc: [DEBUG] image.__init__() (from dwifslpreproc:193): {'_intensity_offset': 0.0, '_format': u'MRtrix', '_transform': [[1.0, 0.0, 0.0, -104.76000893116], [0.0, 0.9988061374039, -0.0488497685184, -74.3036471873993], [-0.0, 0.0488497685184, 0.9988061374039, -86.3906509626887], [0.0, 0.0, 0.0, 1.0]], '_intensity_scale': 1.0, '_datatype': u'Float32LE', '_name': u'dwi.mif', '_keyval': {u'EchoTime': 0.0664, u'RepetitionTime': 3.98, u'mrtrix_version': u'3.0.2-31-g67bf6093', u'FlipAngle': [90, 180], u'PartialFourier': 0.875, u'comments': [u'wk92_3201 (wk92_3201) [MR] DTIcmrr_1.8iso_3shell_b2400_TE66_SMS2_AP', u'study: baecke^Test [ ORIGINAL PRIMARY DIFFUSION NONE MB ND NORM MOSAIC ]', u'DOB: 01/01/1960', u'DOS: 02/04/2019 15:00:11'], u'PhaseEncodingDirection': u'j-', u'MultibandAccelerationFactor': 2, u'SliceEncodingDirection': u'k', u'SliceTiming': [0.0, 1.88, 3.76, 1.6825, 3.5625, 1.485, 3.365, 1.285, 3.1675, 1.0875, 2.9675, 0.89, 2.77, 0.6925, 2.5725, 0.495, 2.375, 0.295, 2.1775, 0.0975, 1.98, 3.86, 1.78, 3.6625, 1.5825, 3.4625, 1.385, 3.265, 1.1875, 3.0675, 0.99, 2.87, 0.79, 2.6725, 0.5925, 2.4725, 0.395, 2.275, 0.1975, 2.0775, 0.0, 1.88, 3.76, 1.6825, 3.5625, 1.485, 3.365, 1.285, 3.1675, 1.0875, 2.9675, 0.89, 2.77, 0.6925, 2.5725, 0.495, 2.375, 0.295, 2.1775, 0.0975, 1.98, 3.86, 1.78, 3.6625, 1.5825, 3.4625, 1.385, 3.265, 1.1875, 3.0675, 0.99, 2.87, 0.79, 2.6725, 0.5925, 2.4725, 0.395, 2.275, 0.1975, 2.0775], u'TotalReadoutTime': 0.0339, u'command_history': [u'mrconvert series_6_DTIcmrr_1.8iso_3shell_b2400_TE66_SMS2_AP/ Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/B_01_DWI_wk92_1.8mm_3172_2019.mif (version=3.0.2-31-g67bf6093)', u'dwidenoise B_01_DWI_wk92_1.8mm_3172_2019.mif B_02_denoised_wk92_1.8mm_3172_2019.mif (version=3.0.2-31-g67bf6093)', u'mrdegibbs B_02_denoised_wk92_1.8mm_3172_2019.mif B_03_denoised_dering_wk92_1.8mm_3172_2019.mif (version=3.0.2-31-g67bf6093)', u"mrconvert B_03_denoised_dering_wk92_1.8mm_3172_2019.mif -coord 3 '1:131' B_04_denoised_withoutFirstB0_AP_wk92_1.8mm_3172_2019.mif (version=3.0.2-31-g67bf6093)", u'/home/miracum/mrtrix3/bin/mrconvert /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/B_04_denoised_withoutFirstB0_AP_wk92_1.8mm_3172_2019.mif /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/dwi.mif -json_export /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/dwi.json -info (version=3.0.2-31-g67bf6093)'], u'dw_scheme': [[0.57735026, -0.57735038, 0.57735032, 5.0], [-0.93799639, 0.18036179, -0.29602784, 265.0], [-0.25487185, -0.966968, 0.00361619, 265.0], [0.26850852, 0.00834691, -0.96324116, 265.0], [-0.51920122, 0.79041028, 0.32508722, 270.0], [0.60796934, 0.48912075, 0.62540734, 270.0], [0.06567493, -0.67067617, 0.738837, 270.0], [0.87254018, 0.23766665, -0.426835, 265.0], [-0.04770676, 0.61473256, 0.78729141, 270.0], [-0.61817431, 0.64060622, -0.45550442, 265.0], [0.57735026, -0.57735038, 0.57735032, 5.0], [-0.00844199, 0.41697538, -0.90887851, 795.0], [-0.00954073, -0.91078699, -0.41276625, 800.0], [0.99899274, 0.01754255, -0.04130214, 800.0], [0.59608793, -0.75320059, 0.27815136, 800.0], [-0.55697346, -0.35443673, -0.75110275, 795.0], [0.62954617, -0.1537956, -0.76158941, 795.0], [0.5848856, 0.79228795, -0.17374842, 800.0], [-0.69784927, 0.26691502, -0.66465235, 795.0], [0.57201278, -0.68423903, -0.45234761, 795.0], [-0.08775683, -0.89342618, 0.44055453, 805.0], [0.03069417, -0.31166795, -0.94969517, 795.0], [0.75991088, 0.37810048, -0.52874893, 795.0], [-0.81626874, -0.49694982, -0.29452717, 800.0], [-0.87618738, 0.47683981, 0.07013749, 800.0], [-0.16620705, 0.98595381, -0.01645165, 800.0], [-0.29868853, 0.0554062, -0.95274091, 795.0], [-0.45341623, -0.79873651, -0.39551723, 800.0], [0.57735026, -0.57735038, 0.57735032, 5.0], [-0.42452773, -0.37482208, 0.8241871, 805.0], [-0.9209404, 0.00791028, -0.38962328, 800.0], [0.22224967, -0.62930661, -0.74470007, 795.0], [-0.26975873, 0.70844209, -0.65218097, 795.0], [-0.88675982, 0.1464432, 0.43841934, 805.0], [-0.86522663, -0.48307237, 0.13425334, 800.0], [-0.23591673, -0.62432283, -0.7446909, 795.0], [-0.38000572, -0.71244895, 0.58992553, 805.0], [0.54081929, -0.83548737, -0.09734078, 800.0], [0.19028635, 0.04629009, -0.98063672, 795.0], [0.8403576, -0.41960761, 0.34311581, 800.0], [-0.26245797, -0.96274799, -0.06505373, 800.0], [0.41725472, -0.40053666, 0.81576282, 805.0], [0.50897622, -0.43284231, -0.74403679, 795.0], [0.77680987, 0.2021421, 0.59640986, 805.0], [0.25485501, -0.90353632, 0.34448692, 805.0], [-0.91732264, -0.16325313, 0.36313558, 800.0], [0.57735026, -0.57735038, 0.57735032, 5.0], [-0.7151261, -0.6389727, -0.28338772, 2395.0], [0.69953507, -0.64524394, -0.30710104, 2395.0], [0.20471382, -0.46842951, 0.85945678, 2410.0], [-0.70392483, -0.26718506, 0.6581049, 2405.0], [0.07683749, 0.52291548, 0.84891433, 2410.0], [-0.03691429, 0.98218513, -0.18425412, 2395.0], [0.87106407, -0.1694538, 0.46101281, 2405.0], [-0.41322556, 0.18808559, 0.890993, 2410.0], [0.53669292, 0.78219616, -0.31643304, 2395.0], [-0.98549527, 0.09847239, 0.138211, 2400.0], [-0.5067274, -0.10754216, -0.85537255, 2390.0], [-0.14192897, 0.91690445, 0.37301761, 2405.0], [-0.54972976, 0.72419852, -0.41633335, 2395.0], [0.57735026, -0.57735038, 0.57735032, 5.0], [0.27551633, 0.55964226, -0.78159529, 2390.0], [0.92677081, 0.3741481, -0.03330019, 2400.0], [-0.32523698, -0.80635041, -0.49398375, 2395.0], [-0.74979568, 0.3021363, 0.58865958, 2405.0], [-0.0381232, 0.02387862, -0.99898756, 2390.0], [-0.82192928, 0.5536052, -0.13399068, 2400.0], [-0.78196025, -0.29278985, -0.55028361, 2395.0], [0.04695667, -0.82578087, 0.56203294, 2405.0], [0.34363219, -0.65634263, -0.67166305, 2395.0], [0.36694175, 0.92868835, 0.05377373, 2400.0], [0.58779222, -0.35824448, 0.72536969, 2410.0], [0.44590971, -0.89479852, -0.02235875, 2400.0], [-0.80228531, -0.45777029, 0.38312486, 2405.0], [0.57735026, -0.57735038, 0.57735032, 5.0], [0.34082696, 0.19555956, -0.91956145, 2390.0], [0.45827392, 0.50191772, 0.73352814, 2410.0], [0.9766016, 0.07120875, 0.20292567, 2400.0], [-0.87912923, 0.00278722, 0.47657546, 2405.0], [0.26533911, 0.84508491, -0.46414116, 2395.0], [-0.13273431, 0.32269147, 0.93715096, 2410.0], [-0.04817256, -0.98719782, -0.15205145, 2400.0], [-0.88953441, 0.42274547, 0.17324825, 2400.0], [0.35044891, -0.17674224, 0.91975427, 2410.0], [-0.71226263, -0.7013545, 0.02799733, 2400.0], [-0.34622052, 0.69174242, -0.6337378, 2395.0], [-0.00798193, 0.76848978, 0.63981217, 2405.0], [0.77544743, -0.45740286, 0.43527442, 2405.0], [0.57735026, -0.57735038, 0.57735032, 5.0], [-0.54308504, -0.54693681, 0.63711745, 2405.0], [-0.45480615, 0.79940784, 0.39255375, 2405.0], [0.73616558, 0.02087326, 0.67647952, 2405.0], [-0.63462621, 0.03127369, 0.77218628, 2410.0], [0.32392678, -0.90786749, 0.26617318, 2405.0], [-0.88059115, -0.38648558, -0.27420464, 2395.0], [-0.2354628, -0.25322038, -0.93831575, 2390.0], [0.07630058, 0.3675378, -0.92687345, 2390.0], [0.55874109, -0.47803265, -0.67771161, 2395.0], [-0.48846912, -0.82825184, -0.27458453, 2395.0], [0.95687282, -0.25682393, 0.13577951, 2400.0], [-0.94116914, -0.19944602, 0.27280381, 2405.0], [0.65967035, -0.75093919, 0.03041869, 2400.0], [0.57735026, -0.57735038, 0.57735032, 5.0], [-0.25278005, -0.94532871, 0.20604758, 2405.0], [-0.60051364, -0.58556086, -0.54452008, 2395.0], [-0.01499894, -0.65237659, 0.7577464, 2410.0], [0.20465028, -0.05136202, -0.97748685, 2390.0], [-0.21907493, 0.96953458, 0.10958306, 2400.0], [0.88642716, -0.27435794, -0.37279308, 2395.0], [0.24154605, 0.67337972, 0.69872403, 2405.0], [0.7273013, 0.63382012, -0.26325819, 2395.0], [-0.59000188, 0.14625072, -0.79404575, 2390.0], [-0.51236099, -0.32176894, 0.79621017, 2410.0], [0.28353515, -0.49025899, -0.82416838, 2390.0], [0.56522822, -0.56330436, 0.60266501, 2405.0], [-0.89909619, -0.10859653, -0.42406702, 2395.0], [0.57735026, -0.57735038, 0.57735032, 5.0], [0.14862876, 0.91822112, 0.36712319, 2405.0], [0.22601262, -0.86431515, 0.44930792, 2405.0], [-0.67151958, 0.55000257, 0.49654663, 2405.0], [-0.98989004, -0.13933425, 0.02652614, 2400.0], [-0.42540705, -0.7169807, 0.55223876, 2405.0], [-0.5908553, -0.29913455, -0.74927193, 2390.0], [0.12369111, -0.24178907, 0.96241289, 2410.0], [0.67555416, -0.69531924, 0.24527054, 2405.0], [0.5389896, 0.84085304, -0.04956008, 2400.0], [-0.24661002, 0.80427885, 0.54066509, 2405.0], [-0.7700237, -0.06002368, 0.63518566, 2405.0], [-0.83604592, -0.54135126, -0.08925267, 2400.0], [-0.26947674, -0.0553134, -0.96141708, 2390.0], [0.57735026, -0.57735038, 0.57735032, 5.0]], u'PixelBandwidth': 2085, u'DiffusionScheme': u'Monopolar'}, '_size': [120, 120, 80, 131], '_spacing': [1.8, 1.8, 1.8, None], '_strides': [-1, -2, 3, 4]}
dwifslpreproc: [DEBUG] execute() (from app.py:197): Number of DWI volumes: 131
dwifslpreproc: [DEBUG] execute() (from app.py:197): Number of DWI slices: 80
dwifslpreproc: [DEBUG] phaseencoding.direction() (from phaseencoding.py:85): j- -> [0, -1, 0]
dwifslpreproc: [DEBUG] phaseencoding.get_scheme() (from dwifslpreproc:200): [0.0, -1.0, 0.0, 0.0339] x 131 rows
dwifslpreproc: [DEBUG] path.name_temporary() (from image.py:33): /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/mrtrix-tmp-jAuaFB.json
dwifslpreproc: [DEBUG] run.exe_name() (from run.py:546): mrinfo -> mrinfo
dwifslpreproc: [DEBUG] run.version_match() (from image.py:34): Version-matched executable for mrinfo: /home/miracum/mrtrix3/bin/mrinfo
dwifslpreproc: [DEBUG] run.exe_name() (from image.py:34): /home/miracum/mrtrix3/bin/mrinfo -> /home/miracum/mrtrix3/bin/mrinfo
dwifslpreproc: Loading header for image file 'se_epi.mif'
dwifslpreproc: [DEBUG] image.__init__() (from dwifslpreproc:202): ['/home/miracum/mrtrix3/bin/mrinfo', 'se_epi.mif', '-json_all', '/mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/mrtrix-tmp-jAuaFB.json']
dwifslpreproc: [DEBUG] image.__init__() (from dwifslpreproc:202): {'_intensity_offset': 0.0, '_format': u'MRtrix', '_transform': [[1.0, 0.0, 0.0, -104.76000893116], [0.0, 0.9988061374039, -0.0488497685184, -74.3036471873993], [-0.0, 0.0488497685184, 0.9988061374039, -86.3906509626887], [0.0, 0.0, 0.0, 1.0]], '_intensity_scale': 1.0, '_datatype': u'Float32LE', '_name': u'se_epi.mif', '_keyval': {u'EchoTime': 0.0664, u'RepetitionTime': 3.98, u'mrtrix_version': u'3.0.2-31-g67bf6093', u'FlipAngle': [90, 180], u'PartialFourier': 0.875, u'comments': [u'wk92_3201 (wk92_3201) [MR] DTIcmrr_1.8iso_3shell_b2400_TE66_SMS2_AP', u'study: baecke^Test [ ORIGINAL PRIMARY DIFFUSION NONE MB ND NORM MOSAIC ]', u'DOB: 01/01/1960', u'DOS: 02/04/2019 15:00:11', u'wk92_3201 (wk92_3201) [MR] DTIcmrr_1.8iso_3shell_b2400_TE66_SMS2_PA', u'study: baecke^Test [ ORIGINAL PRIMARY M MB ND NORM ]', u'DOS: 02/04/2019 15:10:14'], u'MultibandAccelerationFactor': 2, u'SliceEncodingDirection': u'k', u'SliceTiming': [0.0, 1.88, 3.76250005, 1.6825, 3.5625, 1.48500001, 3.36500001, 1.28750002, 3.16750002, 1.09000003, 2.97000003, 0.889999986, 2.77250004, 0.692499995, 2.57249999, 0.495000005, 2.375, 0.297500014, 2.17750001, 0.100000001, 1.98000002, 3.8599999, 1.78250003, 3.6624999, 1.58500004, 3.46499991, 1.38499999, 3.26749992, 1.1875, 3.06750011, 0.99000001, 2.86999989, 0.792500019, 2.6724999, 0.595000029, 2.4749999, 0.395000011, 2.27749991, 0.197500005, 2.07999992, 0.0, 1.88, 3.76250005, 1.6825, 3.5625, 1.48500001, 3.36500001, 1.28750002, 3.16750002, 1.09000003, 2.97000003, 0.889999986, 2.77250004, 0.692499995, 2.57249999, 0.495000005, 2.375, 0.297500014, 2.17750001, 0.100000001, 1.98000002, 3.8599999, 1.78250003, 3.6624999, 1.58500004, 3.46499991, 1.38499999, 3.26749992, 1.1875, 3.06750011, 0.99000001, 2.86999989, 0.792500019, 2.6724999, 0.595000029, 2.4749999, 0.395000011, 2.27749991, 0.197500005, 2.07999992], u'pe_scheme': [[0.0, -1.0, 0.0, 0.0339], [0.0, 1.0, 0.0, 0.0339]], u'command_history': [u'variable', u'mrcat F_01_B0_AP_only_wk92_1.8mm_3172_2019.mif C_04_denoised_PA_OnlyB0_wk92_1.8mm_3172_2019.mif G_01_B0_AP_PA_wk92_1.8mm_3172_2019.mif -axis 3 (version=3.0.2-31-g67bf6093)', u'/home/miracum/mrtrix3/bin/mrconvert /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/G_01_B0_AP_PA_wk92_1.8mm_3172_2019.mif /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/se_epi.mif -info (version=3.0.2-31-g67bf6093)'], u'PixelBandwidth': 2085, u'DiffusionScheme': u'Monopolar'}, '_size': [120, 120, 80, 2], '_spacing': [1.8, 1.8, 1.8, None], '_strides': [-1, -3, 4, 2]}
dwifslpreproc: [DEBUG] phaseencoding.get_scheme() (from dwifslpreproc:206): [[0.0, -1.0, 0.0, 0.0339], [0.0, 1.0, 0.0, 0.0339]]
dwifslpreproc: [DEBUG] phaseencoding.direction() (from dwifslpreproc:312): ap -> [0, -1, 0]
dwifslpreproc: [DEBUG] execute() (from app.py:197): Manual PE direction: [0.0, -1.0, 0.0]
dwifslpreproc: [DEBUG] execute() (from app.py:197): Manual readout time: None
dwifslpreproc: [DEBUG] run.exe_name() (from run.py:546): mrinfo -> mrinfo
dwifslpreproc: [DEBUG] run.version_match() (from image.py:150): Version-matched executable for mrinfo: /home/miracum/mrtrix3/bin/mrinfo
dwifslpreproc: [DEBUG] run.exe_name() (from image.py:150): /home/miracum/mrtrix3/bin/mrinfo -> /home/miracum/mrtrix3/bin/mrinfo
dwifslpreproc: Command: '/home/miracum/mrtrix3/bin/mrinfo dwi.mif -shell_indices' (piping data to local storage)
dwifslpreproc: Result: 0,10,28,46,60,74,88,102,116,130 1,2,3,4,5,6,7,8,9 11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45 47,48,49,50,51,52,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,75,76,77,78,79,80,81,82,83,84,85,86,87,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,117,118,119,120,121,122,123,124,125,126,127,128,129
dwifslpreproc: [DEBUG] execute() (from app.py:197): Manual DWI PE scheme for 'Pair' PE design: [[0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1], [0.0, -1.0, 0.0, 0.1]]
dwifslpreproc: [DEBUG] execute() (from app.py:197): Manual SEEPI PE scheme for 'Pair' PE design: [[0.0, -1.0, 0.0, 0.1], [0.0, 1.0, 0.0, 0.1]]
dwifslpreproc: [DEBUG] execute() (from app.py:197): Index of first b=0 image in DWIs is 0
dwifslpreproc: [DEBUG] image.match() (from dwifslpreproc:515): 'dwi.mif' 'se_epi.mif' image match
dwifslpreproc: [DEBUG] run.exe_name() (from run.py:546): mrinfo -> mrinfo
dwifslpreproc: [DEBUG] run.version_match() (from run.py:330): Version-matched executable for mrinfo: /home/miracum/mrtrix3/bin/mrinfo
dwifslpreproc: [DEBUG] run._shebang() (from run.py:340): File "/home/miracum/mrtrix3/bin/mrinfo": Not a text file
dwifslpreproc: [DEBUG] run.command() (from dwifslpreproc:732): To execute: [['/home/miracum/mrtrix3/bin/mrinfo', 'dwi.mif', '-export_grad_mrtrix', 'grad.b', '-info']]
Command: mrinfo dwi.mif -export_grad_mrtrix grad.b
mrinfo: [INFO] opening image "dwi.mif"...
mrinfo: [INFO] image "dwi.mif" opened with dimensions 120x120x80x131, voxel spacing 1.8x1.8x1.8xnan, datatype Float32LE
mrinfo: [INFO] found 131x4 diffusion gradient table
dwifslpreproc: [DEBUG] run.exe_name() (from run.py:546): mrconvert -> mrconvert
dwifslpreproc: [DEBUG] run.version_match() (from run.py:330): Version-matched executable for mrconvert: /home/miracum/mrtrix3/bin/mrconvert
dwifslpreproc: [DEBUG] run._shebang() (from run.py:340): File "/home/miracum/mrtrix3/bin/mrconvert": Not a text file
dwifslpreproc: [DEBUG] run.command() (from dwifslpreproc:788): To execute: [['/home/miracum/mrtrix3/bin/mrconvert', 'se_epi.mif', 'topup_in.nii', '-strides', '-1,+2,+3,+4', '-export_pe_table', 'topup_datain.txt', '-info']]
Command: mrconvert se_epi.mif topup_in.nii -strides -1,+2,+3,+4 -export_pe_table topup_datain.txt
mrconvert: [INFO] opening image "se_epi.mif"...
mrconvert: [INFO] image "se_epi.mif" opened with dimensions 120x120x80x2, voxel spacing 1.8x1.8x1.8xnan, datatype Float32LE
mrconvert: [INFO] no valid diffusion gradient table found
mrconvert: [INFO] error importing diffusion gradient table for image "se_epi.mif"
mrconvert: [INFO] opening image "-1,+2,+3,+4"...
mrconvert: [INFO] creating image "topup_in.nii"...
mrconvert: [INFO] image "topup_in.nii" created with dimensions 120x120x80x2, voxel spacing 1.8x1.8x1.8xnan, datatype Float32LE
mrconvert: [100%] copying from "se_epi.mif" to "topup_in.nii"
dwifslpreproc: [DEBUG] run.exe_name() (from run.py:339): topup -> topup
dwifslpreproc: [DEBUG] run.version_match() (from run.py:566): Command topup not found in MRtrix3 bin/ directory
dwifslpreproc: [DEBUG] run.exe_name() (from run.py:568): topup -> topup
dwifslpreproc: [DEBUG] run._shebang() (from run.py:340): File "topup": Not a text file
dwifslpreproc: [DEBUG] run.command() (from dwifslpreproc:795): To execute: [['topup', '--imain=topup_in.nii', '--datain=topup_datain.txt', '--out=field', '--fout=field_map.nii.gz', '--config=/usr/local/fsl/etc/flirtsch/b02b0.cnf', '--verbose']]
Command: topup --imain=topup_in.nii --datain=topup_datain.txt --out=field --fout=field_map.nii.gz --config=/usr/local/fsl/etc/flirtsch/b02b0.cnf --verbose
dwifslpreproc: [ERROR] topup --imain=topup_in.nii --datain=topup_datain.txt --out=field --fout=field_map.nii.gz --config=/usr/local/fsl/etc/flirtsch/b02b0.cnf --verbose (dwifslpreproc:795)
dwifslpreproc: [ERROR] Failed command did not provide any output information
dwifslpreproc: [ERROR] For debugging, inspect contents of scratch directory: /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/
dwifslpreproc: Scratch directory retained; location: /mnt/DATEN2/DWI_Luchtmann_2019_Auswertung_Interpolation20202020/04_wk92_20190402_3201/Auswertung_07_v2020_Testb177_MRTrixnew_FSL6.0.4.Zbuntu18_wk92_1.8mm_/dwifslpreproc-tmp-WPH4E7/
miracum@DIZ-UMMD-B175:/$
- The last Command in the log.txt
mrconvert se_epi.mif topup_in.nii -strides -1,+2,+3,+4 -export_pe_table topup_datain.txt
The last Command in the log.txt runs just fine and the result “topup_datain.txt” was already there. So, it must be the Command that comes next.
- May that helps. In the temporary folder there was a file called error.txt. The inside:
topup --imain=topup_in.nii --datain=topup_datain.txt --out=field --fout=field_map.nii.gz --config=/usr/local/fsl/etc/flirtsch/b02b0.cnf --verbose
- If I run this in the temp folder in the terminal it gives me this:
Illegal instruction (core dumped)
I could not find out more so far. maybe you have an idea.
Thanks , Ralf