Hi experts!
When I am using 5ttgen fsl, I get the following error message:
5ttgen: [WARNING] FSL script ‘standard_space_roi’ did not complete successfully; attempting to continue by providing un-cropped image to BET
Command: bet T1.nii T1_BET.nii.gz -f 0.15 -R
5ttgen: [ERROR] Unable to find FSL output file for path “T1_BET.nii.gz”
After using the -debug mode, the following message appears:
5ttgen:
5ttgen: 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.
5ttgen:
5ttgen: [DEBUG] path.script_subdir_name() (from algorithm.py:69): _5ttgen
5ttgen: Generated scratch directory: /work/5ttgen-tmp-89Y288/
5ttgen: [DEBUG] path.from_user() (from fsl.py:47): T1.mif → /work/T1.mif
5ttgen: [DEBUG] path.name_temporary() (from image.py:36): /work/5ttgen-tmp-89Y288/mrtrix-tmp-SR7ejM.json
5ttgen: [DEBUG] run.exe_name() (from run.py:561): mrinfo → mrinfo
5ttgen: [DEBUG] run.version_match() (from image.py:37): Version-matched executable for mrinfo: /opt/mrtrix3/bin/mrinfo
5ttgen: [DEBUG] run.exe_name() (from image.py:37): /opt/mrtrix3/bin/mrinfo → /opt/mrtrix3/bin/mrinfo
5ttgen: Loading header for image file ‘/work/T1.mif’
5ttgen: [DEBUG] image.init() (from image.py:137): [‘/opt/mrtrix3/bin/mrinfo’, ‘/work/T1.mif’, ‘-json_all’, ‘/work/5ttgen-tmp-89Y288/mrtrix-tmp-SR7ejM.json’]
5ttgen: [DEBUG] image.init() (from image.py:137): {‘_name’: ‘/work/T1.mif’, ‘_size’: [160, 256, 256], ‘_spacing’: [1.0, 0.976562, 0.976562], ‘_strides’: [3, -1, -2], ‘_format’: ‘MRtrix’, ‘_datatype’: ‘UInt16LE’, ‘_intensity_offset’: 0.0, ‘_intensity_scale’: 1.0, ‘_transform’: [[0.997840436511461, 0.0583878319888502, 0.030088608114341, -92.4226765634515], [-0.058828112011496, 0.998170502831034, 0.0139606774622304, -108.571813485641], [-0.0292184274008624, -0.0157005845013301, 0.999449736178132, -131.080642721376], [0.0, 0.0, 0.0, 1.0]], ‘_keyval’: {‘EchoTime’: 0.00367, ‘FlipAngle’: [9, 8], ‘InversionTime’: 1.04, ‘PhaseEncodingDirection’: ‘j-’, ‘PixelBandwidth’: 180, ‘RepetitionTime’: 1.91, ‘command_history’: ‘mrconvert T1/ T1.mif (version=3.0.4)’, ‘comments’: [‘Snake_T1 (17.09.13-18:50:37-DST-1.3.12.2.1107.5.2.43.166002) [MR] T1 mp-rage3d we sag 1mm’, ‘study: AG Schwarzbach^SEQUENCE_TESTING [ ORIGINAL PRIMARY M NORM DIS2D ]’, ‘DOB: 15/03/1994’, ‘DOS: 13/09/2017 19:16:10’], ‘mrtrix_version’: ‘3.0.4’}}
5ttgen: [DEBUG] image.check_3d_nonunity() (from fsl.py:47): Image ‘/work/T1.mif’ is >= 3D, and does not contain a unity spatial dimension
5ttgen: [DEBUG] path.from_user() (from fsl.py:48): T1.mif → /work/T1.mif
5ttgen: [DEBUG] path.to_scratch() (from fsl.py:48): input.mif → /work/5ttgen-tmp-89Y288/input.mif
5ttgen: [DEBUG] run.exe_name() (from run.py:561): mrconvert → mrconvert
5ttgen: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrconvert: /opt/mrtrix3/bin/mrconvert
5ttgen: [DEBUG] run._shebang() (from run.py:355): File “/opt/mrtrix3/bin/mrconvert”: Not a text file
5ttgen: [DEBUG] run.command() (from fsl.py:48): To execute: [[‘/opt/mrtrix3/bin/mrconvert’, ‘/work/T1.mif’, ‘/work/5ttgen-tmp-89Y288/input.mif’]]
Command: mrconvert /work/T1.mif /work/5ttgen-tmp-89Y288/input.mif
mrconvert: [INFO] opening image “/work/T1.mif”…
mrconvert: [INFO] image “/work/T1.mif” opened with dimensions 160x256x256, voxel spacing 1x0.97656200000000004x0.97656200000000004, datatype UInt16LE
mrconvert: [INFO] no valid diffusion gradient table found
mrconvert: [INFO] error importing diffusion gradient table for image “/work/T1.mif”
mrconvert: [INFO] creating image “/work/5ttgen-tmp-89Y288/input.mif”…
mrconvert: [INFO] image “/work/5ttgen-tmp-89Y288/input.mif” created with dimensions 160x256x256, voxel spacing 1x0.97656200000000004x0.97656200000000004, datatype UInt16LE
mrconvert: [100%] copying from “/work/T1.mif” to “/work/5ttgen-tmp-89Y288/input.mif”
mrconvert: [INFO] writing back contents of mapped file “/work/5ttgen-tmp-89Y288/input.mif”…
5ttgen: Changing to scratch directory (/work/5ttgen-tmp-89Y288/)
5ttgen: [DEBUG] fsl.exe_name() (from fsl.py:66): bet
5ttgen: [DEBUG] fsl.exe_name() (from fsl.py:67): fast
5ttgen: [DEBUG] fsl.exe_name() (from fsl.py:68): run_first_all
5ttgen: [DEBUG] fsl.exe_name() (from fsl.py:69): standard_space_roi
5ttgen: [DEBUG] fsl.suffix() (from fsl.py:75): NIFTI_GZ → .nii.gz
5ttgen: [DEBUG] path.name_temporary() (from image.py:36): /work/5ttgen-tmp-89Y288/mrtrix-tmp-Mp0Lrd.json
5ttgen: [DEBUG] run.exe_name() (from run.py:561): mrinfo → mrinfo
5ttgen: [DEBUG] run.version_match() (from image.py:37): Version-matched executable for mrinfo: /opt/mrtrix3/bin/mrinfo
5ttgen: [DEBUG] run.exe_name() (from image.py:37): /opt/mrtrix3/bin/mrinfo → /opt/mrtrix3/bin/mrinfo
5ttgen: Loading header for image file ‘input.mif’
5ttgen: [DEBUG] image.init() (from fsl.py:84): [‘/opt/mrtrix3/bin/mrinfo’, ‘input.mif’, ‘-json_all’, ‘/work/5ttgen-tmp-89Y288/mrtrix-tmp-Mp0Lrd.json’]
5ttgen: [DEBUG] image.init() (from fsl.py:84): {‘_name’: ‘input.mif’, ‘_size’: [160, 256, 256], ‘_spacing’: [1.0, 0.976562, 0.976562], ‘_strides’: [3, -1, -2], ‘_format’: ‘MRtrix’, ‘_datatype’: ‘UInt16LE’, ‘_intensity_offset’: 0.0, ‘_intensity_scale’: 1.0, ‘_transform’: [[0.997840436511461, 0.0583878319888502, 0.030088608114341, -92.4226765634515], [-0.058828112011496, 0.998170502831034, 0.0139606774622304, -108.571813485641], [-0.0292184274008624, -0.0157005845013301, 0.999449736178132, -131.080642721376], [0.0, 0.0, 0.0, 1.0]], ‘_keyval’: {‘EchoTime’: 0.00367, ‘FlipAngle’: [9, 8], ‘InversionTime’: 1.04, ‘PhaseEncodingDirection’: ‘j-’, ‘PixelBandwidth’: 180, ‘RepetitionTime’: 1.91, ‘command_history’: [‘mrconvert T1/ T1.mif (version=3.0.4)’, ‘/opt/mrtrix3/bin/mrconvert /work/T1.mif /work/5ttgen-tmp-89Y288/input.mif (version=3.0.4)’], ‘comments’: [‘Snake_T1 (17.09.13-18:50:37-DST-1.3.12.2.1107.5.2.43.166002) [MR] T1 mp-rage3d we sag 1mm’, ‘study: AG Schwarzbach^SEQUENCE_TESTING [ ORIGINAL PRIMARY M NORM DIS2D ]’, ‘DOB: 15/03/1994’, ‘DOS: 13/09/2017 19:16:10’], ‘mrtrix_version’: ‘3.0.4’}}
5ttgen: [DEBUG] run.exe_name() (from run.py:561): mrconvert → mrconvert
5ttgen: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrconvert: /opt/mrtrix3/bin/mrconvert
5ttgen: [DEBUG] run._shebang() (from run.py:355): File “/opt/mrtrix3/bin/mrconvert”: Not a text file
5ttgen: [DEBUG] run.command() (from fsl.py:93): To execute: [[‘/opt/mrtrix3/bin/mrconvert’, ‘input.mif’, ‘T1.nii’, ‘-strides’, ‘-1,+2,+3’]]
Command: mrconvert input.mif T1.nii -strides -1,+2,+3
mrconvert: [INFO] opening image “input.mif”…
mrconvert: [INFO] image “input.mif” opened with dimensions 160x256x256, voxel spacing 1x0.97656200000000004x0.97656200000000004, datatype UInt16LE
mrconvert: [INFO] no valid diffusion gradient table found
mrconvert: [INFO] error importing diffusion gradient table for image “input.mif”
mrconvert: [INFO] opening image “-1,+2,+3”…
mrconvert: [INFO] creating image “T1.nii”…
mrconvert: [INFO] image “T1.nii” created with dimensions 160x256x256, voxel spacing 1x0.97656200000000004x0.97656200000000004, datatype UInt16LE
mrconvert: [100%] copying from “input.mif” to “T1.nii”
mrconvert: [INFO] writing back contents of mapped file “T1.nii”…
5ttgen: [DEBUG] run.exe_name() (from run.py:561): maskfilter → maskfilter
5ttgen: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for maskfilter: /opt/mrtrix3/bin/maskfilter
5ttgen: [DEBUG] run._shebang() (from run.py:355): File “/opt/mrtrix3/bin/maskfilter”: Not a text file
5ttgen: [DEBUG] run.command() (from fsl.py:138): To execute: [[‘/opt/mrtrix3/bin/maskfilter’, ‘/opt/fsl/data/standard/MNI152_T1_1mm_brain_mask_dil.nii.gz’, ‘dilate’, ‘mni_mask.nii’, ‘-npass’, ‘4’]]
Command: maskfilter /opt/fsl/data/standard/MNI152_T1_1mm_brain_mask_dil.nii.gz dilate mni_mask.nii -npass 4
maskfilter: [INFO] opening image “/opt/fsl/data/standard/MNI152_T1_1mm_brain_mask_dil.nii.gz”…
maskfilter: [INFO] Axes and transform of image “/opt/fsl/data/standard/MNI152_T1_1mm_brain_mask_dil.nii.gz” altered to approximate RAS coordinate system
maskfilter: [INFO] image “/opt/fsl/data/standard/MNI152_T1_1mm_brain_mask_dil.nii.gz” opened with dimensions 182x218x182, voxel spacing 1x1x1, datatype Float32LE
maskfilter: [100%] uncompressing image “/opt/fsl/data/standard/MNI152_T1_1mm_brain_mask_dil.nii.gz”
maskfilter: [INFO] creating image “mni_mask.nii”…
maskfilter: [WARNING] requested datatype (Bit) not supported - substituting with UInt8
maskfilter: [INFO] image “mni_mask.nii” created with dimensions 182x218x182, voxel spacing 1x1x1, datatype UInt8
maskfilter: [100%] applying dilate filter to image MNI152_T1_1mm_brain_mask_dil.nii.gz
maskfilter: [INFO] writing back contents of mapped file “mni_mask.nii”…
5ttgen: [DEBUG] run.exe_name() (from run.py:354): standard_space_roi → standard_space_roi
5ttgen: [DEBUG] run.version_match() (from run.py:581): Command standard_space_roi not found in MRtrix3 bin/ directory
5ttgen: [DEBUG] run.exe_name() (from run.py:583): standard_space_roi → standard_space_roi
5ttgen: [DEBUG] run._shebang() (from run.py:355): File “standard_space_roi”: string “#!/bin/sh”: [‘/bin/sh’]
5ttgen: [DEBUG] run.command() (from fsl.py:143): To execute: [[‘/bin/sh’, ‘/opt/fsl/bin/standard_space_roi’, ‘T1.nii’, ‘T1_preBET.nii.gz’, ‘-maskMASK’, ‘mni_mask.nii’, ‘-roiFOV’]]
Command: standard_space_roi T1.nii T1_preBET.nii.gz -maskMASK mni_mask.nii -roiFOV
/opt/fsl/bin/flirt: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/convert_xfm: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslhd: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
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/opt/fsl/bin/fslhd: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
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/opt/fsl/bin/fslhd: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
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/opt/fsl/bin/fslmaths: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/flirt: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslmaths: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslmaths: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslmaths: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/flirt: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslstats: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslroi: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/bin/rm: cannot remove ‘T1_preBET_tmp*’: No such file or directory
5ttgen: [WARNING] FSL script ‘standard_space_roi’ did not complete successfully; attempting to continue by providing un-cropped image to BET
5ttgen: [DEBUG] run.exe_name() (from run.py:354): bet → bet
5ttgen: [DEBUG] run.version_match() (from run.py:581): Command bet not found in MRtrix3 bin/ directory
5ttgen: [DEBUG] run.exe_name() (from run.py:583): bet → bet
5ttgen: [DEBUG] run._shebang() (from run.py:355): File “bet”: string “#!/bin/sh”: [‘/bin/sh’]
5ttgen: [DEBUG] run.command() (from fsl.py:157): To execute: [[‘/bin/sh’, ‘/opt/fsl/bin/bet’, ‘T1.nii’, ‘T1_BET.nii.gz’, ‘-f’, ‘0.15’, ‘-R’]]
Command: bet T1.nii T1_BET.nii.gz -f 0.15 -R
/opt/fsl/bin/fslhd: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslhd: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslhd: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslhd: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslhd: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslhd: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/bet2: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslstats: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/bet2: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslstats: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
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/opt/fsl/bin/bet2: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslstats: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
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/opt/fsl/bin/bet2: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslstats: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
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/opt/fsl/bin/bet2: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslstats: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
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/opt/fsl/bin/bet2: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslstats: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
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/opt/fsl/bin/bet2: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslstats: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
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/opt/fsl/bin/bet2: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslstats: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
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/opt/fsl/bin/bet2: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslstats: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
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/opt/fsl/bin/bet2: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslstats: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
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/opt/fsl/bin/bet2: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/opt/fsl/bin/fslstats: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
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5ttgen: [ERROR] Unable to find FSL output file for path “T1_BET.nii.gz”
What should I do to solve the problem?