Dwifslpreproc:795

Hi MRTrixler,

I have two systems. Both worked fine. Both have the same newest MRTrix Version but a different in the FSL version. (6.0.4 and 6.0.1.)…
On the older one my Batch is running and on the newer one… both use the same data…
Looks like an fsl problem.
I get that error:


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)

Command:

dwifslpreproc B_04.mif B_05.mif -pe_dir AP -rpe_pair -se_epi G_01.mif -eddy_options "--data_is_shelled --slm=linear"

And there is a difference in the Ubuntu Version… Its working on focal 20.04 and isnt working on groovy 20.10. Maybe this could be the point? Dont know. Its not a big difference.
What does the Error mean and how can I change that. What xould be the problem?
Thanks for any help or hint or advice,

Ralf

Hi,

I have no idea yet. I installed some machines with Ubuntu 18 and 20 and FSL 6.0.1 and 6.0.4 and can say so far that it is running on MRTrix 3.0.2-25g24b61f68 very well and on 3.0.2-31-g67bf6093 not.
Is there a way to go back (ckeck out) to MRTrix 3.0.2-25. So I could install it on all my machines for the next weeks to calculate the study.

Thanks,

Ralf

Hi Ralf,

Sorry if this comes too late, but just in case:

I’m not sure what’s causing the error, but one thing I find odd is the lack of any output from topup itself – that should also be shown on the terminal if there’s an error. To figure out what’s going on, you could try something like this:

  • run your command with the -nocleanup and -debug options to allow inspection of intermediate data and view full debugging output respectively. Post the full terminal output here for us to inspect.

  • look in the temporary folder created by the command (its location will be reported on the terminal), and check the log.txt file to see the list of commands executed to get to that point. Hopefully the last one shown will be the problematic topup call. Copy/paste that line into your terminal to see whether that same command runs successfully when invoked directly, and if not, observe exactly how it fails. Report any error messages that manual run might produce on the terminal.

Hopefully that’ll provide a clearer hint as to what might be causing the issue…

Hi Donald,

I hope I did it right:

  1. 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
  1. 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, 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[-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, 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-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:/$ 
  1. 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.

  1. 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
  1. 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

OK, this is the one to focus on. What this says is that this version of topup is issuing CPU instructions that your CPU doesn’t understand. My guess is it’s been compiled and optimised for a CPU architecture that is a few generations ahead of yours. What system are you running this on? What does lscpu report on the affected system? And where did the problematic version of topup come from? Can you get any information about how it was compiled…?

lscpu gives me this:

Architecture:        x86_64
CPU op-mode(s):      32-bit, 64-bit
Byte Order:          Little Endian
CPU(s):              8
On-line CPU(s) list: 0-7
Thread(s) per core:  1
Core(s) per socket:  4
Socket(s):           2
NUMA node(s):        1
Vendor ID:           AuthenticAMD
CPU family:          15
Model:               6
Model name:          Common KVM processor
Stepping:            1
CPU MHz:             1996.250
BogoMIPS:            3992.50
Hypervisor vendor:   KVM
Virtualization type: full
L1d cache:           64K
L1i cache:           64K
L2 cache:            512K
L3 cache:            16384K
NUMA node0 CPU(s):   0-7
Flags:               fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx lm rep_good nopl cpuid extd_apicid tsc_known_freq pni cx16 x2apic hypervisor cmp_legacy 3dnowprefetch vmmcall

Topup Version:
Part of FSL (ID: 6.0.4:ddd0a010)

I tried the normal Installation of FSL 6.0.1 and 6.0.4 with Ubuntu 18 and Ubuntu 20. All gave the same problem. Is it the problem that it runs on AMD maybe?

Ralf

Hi, sorry for the late answer. It took me a while to figure it out and test it.
It works on Intel fine:

Architektur:                     x86_64
CPU Operationsmodus:             32-bit, 64-bit
Byte-Reihenfolge:                Little Endian
Adressgrößen:                    40 bits physical, 48 bits virtual
CPU(s):                          8
Liste der Online-CPU(s):         0-7
Thread(s) pro Kern:              1
Kern(e) pro Socket:              4
Sockel:                          2
NUMA-Knoten:                     1
Anbieterkennung:                 GenuineIntel
Prozessorfamilie:                6
Modell:                          44
Modellname:                      Westmere E56xx/L56xx/X56xx (Nehalem-C)
Stepping:                        1
CPU MHz:                         1996.250
BogoMIPS:                        3992.50
Hypervisor-Anbieter:             KVM
Virtualisierungstyp:             voll
L1d Cache:                       256 KiB
L1i Cache:                       256 KiB
L2 Cache:                        32 MiB
L3 Cache:                        32 MiB
NUMA-Knoten0 CPU(s):             0-7
Vulnerability Itlb multihit:     KVM: Mitigation: VMX unsupported

At least I know what works and what isnt, so I can handle it.

Thanks for the help and bringing me closer to the problem.

Ralf

I’m not sure, but it looks like your AMD setup is running on a kernel-based Virtual Machine, and there’s a chance the CPU model selected doesn’t expose all the features of your CPU to the guest OS. I’ve no idea how much control you might have over this, and whether you can select a CPU model that is closer to your actual hardware CPU, which might then expose the expected instructions (assuming your CPU does indeed implement them!).

Maybe this is in fact what you did with your Intel results…? I note it still looks like it’s running on a KVM…