Hi,
I have inherited a project from a colleague, which involved using 5ttgen fsl to classify tisue. I have set up fsl and mrtrix on my computer (ubuntu 18.04), but when I run the same command that works on his computer (and using the same dataset) on my computer, it hangs indefinetly. I suspected that this had to do with with the program not finding the right files in the MRtrix/bin folder, so I added that to the PATH, but it still does not work. I would be grateful if you can help me troubleshoot this problem.
aelkady@rutland:~/work/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii$ echo $PATH
/export02/data/Toolboxes/mrtrix3/bin:/usr/share/fsl/5.0/bin:/export02/data/Toolboxes/mrtrix3/bin:/home/bic/aelkady/bin:/opt/minc/1.9.16/bin:/opt/minc/1.9.16/p
ipeline:/opt/sge/bin:/opt/sge/bin/lx-amd64:/home/bic/aelkady/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/local/mni/b
in:/usr/local/matlab/bin:/opt/bin:/usr/games
aelkady@rutland:~/work/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii$ source /usr/share/fsl/5.0/etc/fslconf/fsl.sh; export FSLDIR=/usr/share/fsl/5.0; expo
rt PATH=/usr/share/fsl/5.0/bin:${PATH}; export PATH=/export02/data/Toolboxes/mrtrix3/bin:${PATH}; cd ~/Desktop/work/Tim/data/20190326_invivowavecaipi_m-m_005_
m12/nii; 5ttgen fsl 20190326_075937mnigre3DT1wPreGds028a1001.nii.gz 5ttgenOut.nii.gz -debug -nocrop -force ;
5ttgen:
5ttgen: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please c
onsult the help page (-help option) for more information.
5ttgen:
5ttgen: [DEBUG] path.scriptSubDirName() (from algorithm.py:52): _5ttgen
5ttgen: Generated temporary directory: /export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/5ttgen-tmp-66TSZP/
5ttgen: [DEBUG] path.fromUser() (from fsl.py:24): 20190326_075937mnigre3DT1wPreGds028a1001.nii.gz -> /export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_
m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii.gz
5ttgen: [DEBUG] path.newTemporary() (from image.py:11): /export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/5ttgen-tmp-66TSZP/mrtrix-tmp-U3F0L5.j
son
5ttgen: [DEBUG] run.exeName() (from run.py:349): mrinfo -> mrinfo
5ttgen: [DEBUG] run.versionMatch() (from image.py:12): Version-matched executable for mrinfo: /export02/data/Toolboxes/mrtrix3/bin/mrinfo
5ttgen: [DEBUG] run.exeName() (from image.py:12): /export02/data/Toolboxes/mrtrix3/bin/mrinfo -> /export02/data/Toolboxes/mrtrix3/bin/mrinfo
5ttgen: Loading header for image file '/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii.gz'
5ttgen: [DEBUG] image.__init__() (from image.py:105): ['/export02/data/Toolboxes/mrtrix3/bin/mrinfo', '/export02/data/Tim/data/20190326_invivowavecaipi_m-m_00
5_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii.gz', '-json_all', '/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/5ttgen-tmp-66TSZP/m
rtrix-tmp-U3F0L5.json']
5ttgen: [DEBUG] image.__init__() (from image.py:105): {'_intensity_offset': 0.0, '_format': u'NIfTI-1.1 (GZip compressed)', '_transform': [[1.0, 0.0, 0.0, -90
.4662628173828], [-0.0, 0.982287250364135, -0.18738131649678, -102.33479309082], [-0.0, 0.18738131649678, 0.982287250364135, -115.826759338379], [0.0, 0.0, 0.
0, 1.0]], '_intensity_scale': 1.0, '_datatype': u'Int16LE', '_name': u'/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3
DT1wPreGds028a1001.nii.gz', '_keyval': {u'comments': u'irl_a_gre_helms\nTE=4.920000076;sec=32954.8475;phaseDir=+'}, '_size': [192, 256, 192], '_spacing': [1.0
, 1.0, 1.0], '_strides': [-1, 2, 3]}
5ttgen: [DEBUG] image.check3DNonunity() (from fsl.py:24): Image '/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPr
eGds028a1001.nii.gz' is >= 3D, and does not contain a unity spatial dimension
5ttgen: [DEBUG] path.fromUser() (from fsl.py:25): 20190326_075937mnigre3DT1wPreGds028a1001.nii.gz -> /export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_
m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii.gz
5ttgen: [DEBUG] path.toTemp() (from fsl.py:25): input.mif -> /export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/5ttgen-tmp-66TSZP/input.mif
5ttgen: [DEBUG] run.exeName() (from run.py:349): mrconvert -> mrconvert
5ttgen: [DEBUG] run.versionMatch() (from run.py:57): Version-matched executable for mrconvert: /export02/data/Toolboxes/mrtrix3/bin/mrconvert
5ttgen: [DEBUG] run._shebang() (from run.py:67): File "/export02/data/Toolboxes/mrtrix3/bin/mrconvert": Not a text file
5ttgen: [DEBUG] run.command() (from fsl.py:25): To execute: [['/export02/data/Toolboxes/mrtrix3/bin/mrconvert', '/export02/data/Tim/data/20190326_invivowaveca
ipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii.gz', '/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/5ttgen-tmp-66TSZP/inpu
t.mif', '-info']]
Command: mrconvert /export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii.gz /export02/data/Tim/data/2
0190326_invivowavecaipi_m-m_005_m12/nii/5ttgen-tmp-66TSZP/input.mif
mrconvert: [INFO] opening image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii.gz"..
.
mrconvert: [INFO] Axes and transform of image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a
1001.nii.gz" altered to approximate RAS coordinate system
mrconvert: [INFO] image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii.gz" opened wi
th dimensions 192x256x192, voxel spacing 1x1x1, datatype Int16LE
mrconvert: [ 0%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 3%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 6%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 8%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 11%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 14%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 17%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 19%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 22%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 25%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 28%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 31%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 33%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 36%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 39%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 42%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 44%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 47%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 50%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 53%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 56%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 58%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 61%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 64%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 67%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 69%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 72%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 75%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 78%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 81%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 83%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 86%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 89%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 92%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 94%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [ 97%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
mrconvert: [100%] uncompressing image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii
.gz"
mrconvert: [INFO] creating image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/5ttgen-tmp-66TSZP/input.mif"...
mrconvert: [INFO] image "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/5ttgen-tmp-66TSZP/input.mif" created with dimensions 192x2
56x192, voxel spacing 1x1x1, datatype Int16LE
mrconvert: [100%] copying from "/export02/...e3DT1wPreGds028a1001.nii.gz" to "/export02/...5ttgen-tmp-66TSZP/input.mif"
5ttgen: Changing to temporary directory (/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/5ttgen-tmp-66TSZP/)
5ttgen: [DEBUG] fsl.exeName() (from fsl.py:47): fsl5.0-bet
5ttgen: [DEBUG] fsl.exeName() (from fsl.py:48): fsl5.0-fast
5ttgen: [DEBUG] fsl.exeName() (from fsl.py:49): fsl5.0-run_first_all
5ttgen: [DEBUG] fsl.exeName() (from fsl.py:50): fsl5.0-standard_space_roi
5ttgen: [DEBUG] fsl.suffix() (from fsl.py:56): NIFTI_GZ -> .nii.gz
5ttgen: [DEBUG] path.newTemporary() (from image.py:11): /export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12/nii/5ttgen-tmp-66TSZP/mrtrix-tmp-LVUYAK.j
son
5ttgen: [DEBUG] run.exeName() (from run.py:349): mrinfo -> mrinfo
5ttgen: [DEBUG] run.versionMatch() (from image.py:12): Version-matched executable for mrinfo: /export02/data/Toolboxes/mrtrix3/bin/mrinfo
5ttgen: [DEBUG] run.exeName() (from image.py:12): /export02/data/Toolboxes/mrtrix3/bin/mrinfo -> /export02/data/Toolboxes/mrtrix3/bin/mrinfo
5ttgen: Loading header for image file 'input.mif'
5ttgen: [DEBUG] image.__init__() (from fsl.py:62): ['/export02/data/Toolboxes/mrtrix3/bin/mrinfo', 'input.mif', '-json_all', '/export02/data/Tim/data/20190326
_invivowavecaipi_m-m_005_m12/nii/5ttgen-tmp-66TSZP/mrtrix-tmp-LVUYAK.json']
5ttgen: [DEBUG] image.__init__() (from fsl.py:62): {'_intensity_offset': 0.0, '_format': u'MRtrix', '_transform': [[1.0, 0.0, 0.0, -90.4662628173828], [-0.0,
0.982287250364135, -0.18738131649678, -102.33479309082], [-0.0, 0.18738131649678, 0.982287250364135, -115.826759338379], [0.0, 0.0, 0.0, 1.0]], '_intensity_sc
ale': 1.0, '_datatype': u'Int16LE', '_name': u'input.mif', '_keyval': {u'command_history': u'/export02/data/Toolboxes/mrtrix3/bin/mrconvert "/export02/data/Ti
m/data/20190326_invivowavecaipi_m-m_005_m12/nii/20190326_075937mnigre3DT1wPreGds028a1001.nii.gz" "/export02/data/Tim/data/20190326_invivowavecaipi_m-m_005_m12
/nii/5ttgen-tmp-66TSZP/input.mif" "-info" (version=3.0_RC3-135-g2b8e7d0c)', u'mrtrix_version': u'3.0_RC3-135-g2b8e7d0c', u'comments': u'irl_a_gre_helms\nTE=4
.920000076;sec=32954.8475;phaseDir=+'}, '_size': [192, 256, 192], '_spacing': [1.0, 1.0, 1.0], '_strides': [-1, 2, 3]}
5ttgen: [DEBUG] run.exeName() (from run.py:349): mrconvert -> mrconvert
5ttgen: [DEBUG] run.versionMatch() (from run.py:57): Version-matched executable for mrconvert: /export02/data/Toolboxes/mrtrix3/bin/mrconvert
5ttgen: [DEBUG] run._shebang() (from run.py:67): File "/export02/data/Toolboxes/mrtrix3/bin/mrconvert": Not a text file
5ttgen: [DEBUG] run.command() (from fsl.py:71): To execute: [['/export02/data/Toolboxes/mrtrix3/bin/mrconvert', 'input.mif', 'T1.nii', '-strides', '-1,+2,+3',
'-info']]
Command: mrconvert input.mif T1.nii -strides -1,+2,+3
mrconvert: [INFO] opening image "input.mif"...
mrconvert: [INFO] image "input.mif" opened with dimensions 192x256x192, voxel spacing 1x1x1, datatype Int16LE
mrconvert: [INFO] opening image "-1,+2,+3"...
mrconvert: [INFO] creating image "T1.nii"...
mrconvert: [INFO] image "T1.nii" created with dimensions 192x256x192, voxel spacing 1x1x1, datatype Int16LE
mrconvert: [100%] copying from "input.mif" to "T1.nii"
5ttgen: [DEBUG] run.exeName() (from run.py:349): maskfilter -> maskfilter
5ttgen: [DEBUG] run.versionMatch() (from run.py:57): Version-matched executable for maskfilter: /export02/data/Toolboxes/mrtrix3/bin/maskfilter
5ttgen: [DEBUG] run._shebang() (from run.py:67): File "/export02/data/Toolboxes/mrtrix3/bin/maskfilter": Not a text file
5ttgen: [DEBUG] run.command() (from fsl.py:115): To execute: [['/export02/data/Toolboxes/mrtrix3/bin/maskfilter', '/usr/share/fsl/5.0/data/standard/MNI152_T1_
1mm_brain_mask_dil.nii.gz', 'dilate', 'mni_mask.nii', '-npass', '4', '-info']]
Command: maskfilter /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain_mask_dil.nii.gz dilate mni_mask.nii -npass 4
maskfilter: [INFO] opening image "/usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain_mask_dil.nii.gz"...
maskfilter: [INFO] Axes and transform of image "/usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain_mask_dil.nii.gz" altered to approximate RAS coo
rdinate system
maskfilter: [INFO] image "/usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain_mask_dil.nii.gz" opened with dimensions 182x218x182, voxel spacing 1x
1x1, datatype Float32LE
maskfilter: [100%] uncompressing image "/usr/share/fsl/5.0/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
5ttgen: [DEBUG] run.exeName() (from run.py:66): fsl5.0-standard_space_roi -> fsl5.0-standard_space_roi
5ttgen: [DEBUG] run.versionMatch() (from run.py:373): Command fsl5.0-standard_space_roi not found in MRtrix3 bin/ directory
5ttgen: [DEBUG] run.exeName() (from run.py:375): fsl5.0-standard_space_roi -> fsl5.0-standard_space_roi
5ttgen: [DEBUG] run._shebang() (from run.py:67): File "fsl5.0-standard_space_roi": string "#! /bin/sh -e": ['/bin/sh', '-e']
5ttgen: [DEBUG] run.command() (from fsl.py:120): To execute: [['/bin/sh', '-e', '/usr/bin/fsl5.0-standard_space_roi', 'T1.nii', 'T1_preBET.nii.gz', '-maskMASK
', 'mni_mask.nii', '-roiNONE']]
Command: fsl5.0-standard_space_roi T1.nii T1_preBET.nii.gz -maskMASK mni_mask.nii -roiNONE
5ttgen: [DEBUG] fsl.findImage() (from fsl.py:123): Image at expected location: "T1_preBET.nii.gz"
5ttgen: [DEBUG] run.exeName() (from run.py:66): fsl5.0-bet -> fsl5.0-bet
5ttgen: [DEBUG] run.versionMatch() (from run.py:373): Command fsl5.0-bet not found in MRtrix3 bin/ directory
5ttgen: [DEBUG] run.exeName() (from run.py:375): fsl5.0-bet -> fsl5.0-bet
5ttgen: [DEBUG] run._shebang() (from run.py:67): File "fsl5.0-bet": string "#! /bin/sh -e": ['/bin/sh', '-e']
5ttgen: [DEBUG] run.command() (from fsl.py:126): To execute: [['/bin/sh', '-e', '/usr/bin/fsl5.0-bet', 'T1_preBET.nii.gz', 'T1_BET.nii.gz', '-f', '0.15', '-R'
]]
Command: fsl5.0-bet T1_preBET.nii.gz T1_BET.nii.gz -f 0.15 -R
5ttgen: [DEBUG] fsl.findImage() (from fsl.py:127): Image at expected location: "T1_BET.nii.gz"
5ttgen: [DEBUG] run.exeName() (from run.py:66): fsl5.0-fast -> fsl5.0-fast
5ttgen: [DEBUG] run.versionMatch() (from run.py:373): Command fsl5.0-fast not found in MRtrix3 bin/ directory
5ttgen: [DEBUG] run.exeName() (from run.py:375): fsl5.0-fast -> fsl5.0-fast
5ttgen: [DEBUG] run._shebang() (from run.py:67): File "fsl5.0-fast": string "#! /bin/sh -e": ['/bin/sh', '-e']
5ttgen: [DEBUG] run.command() (from fsl.py:143): To execute: [['/bin/sh', '-e', '/usr/bin/fsl5.0-fast', 'T1_BET.nii.gz']]
Command: fsl5.0-fast T1_BET.nii.gz
5ttgen: [DEBUG] run.exeName() (from run.py:66): fsl5.0-run_first_all -> fsl5.0-run_first_all
5ttgen: [DEBUG] run.versionMatch() (from run.py:373): Command fsl5.0-run_first_all not found in MRtrix3 bin/ directory
5ttgen: [DEBUG] run.exeName() (from run.py:375): fsl5.0-run_first_all -> fsl5.0-run_first_all
5ttgen: [DEBUG] run._shebang() (from run.py:67): File "fsl5.0-run_first_all": string "#! /bin/sh -e": ['/bin/sh', '-e']
5ttgen: [DEBUG] run.command() (from fsl.py:160): To execute: [['/bin/sh', '-e', '/usr/bin/fsl5.0-run_first_all', '-m', 'none', '-s', 'L_Accu,R_Accu,L_Caud,R_C
aud,L_Pall,R_Pall,L_Puta,R_Puta,L_Thal,R_Thal', '-i', 'T1.nii', '-o', 'first', '-v']]
Command: fsl5.0-run_first_all -m none -s L_Accu,R_Accu,L_Caud,R_Caud,L_Pall,R_Pall,L_Puta,R_Puta,L_Thal,R_Thal -i T1.nii -o first -v
5ttgen: FSL FIRST job has been submitted to SGE; awaiting completion
5ttgen: (note however that FIRST may fail silently, and hence this script may hang indefinitely)
5ttgen: [DEBUG] file.waitFor() (from fsl.py:17): ['first-L_Accu_first.vtk', 'first-R_Accu_first.vtk', 'first-L_Caud_first.vtk', 'first-R_Caud_first.vtk', 'fir
st-L_Pall_first.vtk', 'first-R_Pall_first.vtk', 'first-L_Puta_first.vtk', 'first-R_Puta_first.vtk', 'first-L_Thal_first.vtk', 'first-R_Thal_first.vtk']
5ttgen: [ 0%] Waiting for creation of 10 new items...