Hello everybody,
When I use 5ttgen to segment my T1 image using fsl method, during the processing it shows this error:
[ERROR] Unable to find FSL output file for path “T1_preBET”
How should I manage this error and problem?
Thanks
Sorry for the lack of response – we’ve all been busy with ISMRM and the workshop…
Could you post the full output of the 5ttgen command, including the command itself? Preferably with the -debug option if possible. The chances are there’ll be some clues at to what went wrong earlier in the output.
I’d also recommend using the -nocleanup option so you can inspect all the intermediate outputs to figure out what happened.
Thank you for your response. I think the problem was in FSL installation. The FSL “standard” folder and all of its files were missing in the installation path. So I downloaded and copied them manually and problem solved.
OK, so it looks as though the FSL command standard_space_roi failed due to the standard space images not being installed, but 5ttgen fsl has historically been made permissive of that particular command failing due to other issues people have experienced with it. You should however have received a warning at the terminal indicating that that particular command had failed, prior to encountering the error itself?
Glad you’ve managed to fix your installation and get the script working, but it looks like with other changes I’ve made to the script it’s no longer compatible with the prospect of that command failing. So I’ll need to re-think my approach there.
Hi, could you please specify which fsl data exactly you downloaded from where and copied it to which specific location?
I’m receiving the same error after installing fsl-complete via neurodebian
on ubuntu 16.04 LTS with the command:
5ttgen fsl t1.mif 5tt.mif -debug
-debug output in summary…:
Summary
> bwgig@bwgchariteIG:~/Schreibtisch/rTMS/data/180629_0946$ 5ttgen fsl t1.mif 5tt_l.mif -debug
> 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.scriptSubDirName() (from algorithm.py:52): _5ttgen
> 5ttgen: Generated temporary directory: /home/bwgig/Schreibtisch/rTMS/data/180629_0946/5ttgen-tmp-3M2B1W/
> 5ttgen: [DEBUG] path.fromUser() (from fsl.py:24): t1.mif -> /home/bwgig/Schreibtisch/rTMS/data/180629_0946/t1.mif
> 5ttgen: [DEBUG] path.newTemporary() (from image.py:11): /home/bwgig/Schreibtisch/rTMS/data/180629_0946/5ttgen-tmp-3M2B1W/mrtrix-tmp-DQ3Q9O.json
> 5ttgen: [DEBUG] run.exeName() (from run.py:351): mrinfo -> mrinfo
> 5ttgen: [DEBUG] run.versionMatch() (from image.py:12): Version-matched executable for mrinfo: /home/bwgig/mrtrix3/bin/mrinfo
> 5ttgen: [DEBUG] run.exeName() (from image.py:12): /home/bwgig/mrtrix3/bin/mrinfo -> /home/bwgig/mrtrix3/bin/mrinfo
> 5ttgen: Loading header for image file '/home/bwgig/Schreibtisch/rTMS/data/180629_0946/t1.mif'
> 5ttgen: [DEBUG] image.__init__() (from image.py:101): ['/home/bwgig/mrtrix3/bin/mrinfo', '/home/bwgig/Schreibtisch/rTMS/data/180629_0946/t1.mif', '-json_all', '/home/bwgig/Schreibtisch/rTMS/data/180629_0946/5ttgen-tmp-3M2B1W/mrtrix-tmp-DQ3Q9O.json']
> 5ttgen: [DEBUG] image.__init__() (from image.py:101): {'_intensity_offset': 0.0, '_format': u'MRtrix', '_transform': [[0.995126049999522, -0.0951284235521, 0.025975520107249, -81.217260721004], [0.0827279841754891, 0.94871820186333, 0.305106299652209, -150.283410323083], [-0.0536677300303433, -0.3014703243865, 0.951963979501165, -130.97506784022], [0.0, 0.0, 0.0, 1.0]], '_intensity_scale': 1.0, '_datatype': u'UInt16LE', '_name': u'/home/bwgig/Schreibtisch/rTMS/data/180629_0946/t1.mif', '_keyval': {u'EchoTime': u'0.00494', u'RepetitionTime': u'2.53', u'mrtrix_version': u'3.0_RC3-51-g52a2540d', u'FlipAngle': u'7', u'comments': u'VP_9 (VP_9) [MR] MPRAGE_freesurfer\nstudy: PICHT 226_TMSNAVI [ ORIGINAL PRIMARY M ND NORM ]\nDOB: 11/05/1993\nDOS: 29/06/2018 10:03:12', u'PhaseEncodingDirection': u'j-', u'TotalReadoutTime': u'0', u'command_history': u'mrconvert "/home/bwgig/Schreibtisch/rTMS Studie Melina/MRT Daten/180629_0946/003_MPRAGE_freesurfer" "t1.mif" (version=3.0_RC3-51-g52a2540d)'}, '_size': [176, 256, 256], '_spacing': [1.0, 1.0, 1.0], '_strides': [3, -1, -2]}
> 5ttgen: [DEBUG] image.check3DNonunity() (from fsl.py:24): Image '/home/bwgig/Schreibtisch/rTMS/data/180629_0946/t1.mif' is >= 3D, and does not contain a unity spatial dimension
> 5ttgen: [DEBUG] path.fromUser() (from fsl.py:25): t1.mif -> /home/bwgig/Schreibtisch/rTMS/data/180629_0946/t1.mif
> 5ttgen: [DEBUG] path.toTemp() (from fsl.py:25): input.mif -> /home/bwgig/Schreibtisch/rTMS/data/180629_0946/5ttgen-tmp-3M2B1W/input.mif
> 5ttgen: [DEBUG] run.exeName() (from run.py:351): mrconvert -> mrconvert
> 5ttgen: [DEBUG] run.versionMatch() (from run.py:57): Version-matched executable for mrconvert: /home/bwgig/mrtrix3/bin/mrconvert
> 5ttgen: [DEBUG] run._shebang() (from run.py:67): File "/home/bwgig/mrtrix3/bin/mrconvert": Not a text file
> 5ttgen: [DEBUG] run.command() (from fsl.py:25): To execute: [['/home/bwgig/mrtrix3/bin/mrconvert', '/home/bwgig/Schreibtisch/rTMS/data/180629_0946/t1.mif', '/home/bwgig/Schreibtisch/rTMS/data/180629_0946/5ttgen-tmp-3M2B1W/input.mif', '-info']]
> Command: mrconvert /home/bwgig/Schreibtisch/rTMS/data/180629_0946/t1.mif /home/bwgig/Schreibtisch/rTMS/data/180629_0946/5ttgen-tmp-3M2B1W/input.mif
> mrconvert: [INFO] opening image "/home/bwgig/Schreibtisch/rTMS/data/180629_0946/t1.mif"...
> mrconvert: [INFO] image "/home/bwgig/Schreibtisch/rTMS/data/180629_0946/t1.mif" opened with dimensions 176x256x256, voxel spacing 1x1x1, datatype UInt16LE
> mrconvert: [INFO] creating image "/home/bwgig/Schreibtisch/rTMS/data/180629_0946/5ttgen-tmp-3M2B1W/input.mif"...
> mrconvert: [INFO] image "/home/bwgig/Schreibtisch/rTMS/data/180629_0946/5ttgen-tmp-3M2B1W/input.mif" created with dimensions 176x256x256, voxel spacing 1x1x1, datatype UInt16LE
> mrconvert: [ 0%] copying from "/home/bwgi...TMS/data/180629_0946/t1.m mrconvert: [ 1%] copying from "/home/bwgi...TMS/data/180629_0946/t1.m mrconvert: [ 2%] copying from "/home/bwgi...TMS/data/180629_0946/t1.m mrconvert: [ 3%] copying from "/home/bwgi...TMS/data/180629_0946/t1.m mrconvert: [ 5%] copying from "/home/bwgi...TMS/data/180629_0946/t1.m mrconvert: [ 6%] copying from "/home/bwgi...TMS/data/180629_0946/t1.m mrconvert: [ 7%] copying from "/home/bwgi...TMS/data/180629_0946/t1.m mrconvert: [ 9%] copying from "/home/bwgi...TMS/data/180629_0946/t1.m mrconvert: [ 10%] copying from "/home/bwgi...TMS/data/180629_0946/t1.m mrconvert: [ 11%] copying from "/home/bwgi...TMS/data/180629_0946/t1.m mrconvert: [ 13%] copying from "/home/bwgi...TMS/data/180629_0946/t1.m mrconvert: [ 14%] copying from "/home/bwgi...TMS/data/180629_0946/t1.m mrconvert: [ 15%] copying from "/home/bwgi...TMS/data/180629_0946/t1.m mrconvert: [ 16%] copying from "/home/bwgi...TMS/data/180629_0946/t1.m mrconvert: [ 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> 5ttgen: Changing to temporary directory (/home/bwgig/Schreibtisch/rTMS/data/180629_0946/5ttgen-tmp-3M2B1W/)
> 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): /home/bwgig/Schreibtisch/rTMS/data/180629_0946/5ttgen-tmp-3M2B1W/mrtrix-tmp-XY3Y8N.json
> 5ttgen: [DEBUG] run.exeName() (from run.py:351): mrinfo -> mrinfo
> 5ttgen: [DEBUG] run.versionMatch() (from image.py:12): Version-matched executable for mrinfo: /home/bwgig/mrtrix3/bin/mrinfo
> 5ttgen: [DEBUG] run.exeName() (from image.py:12): /home/bwgig/mrtrix3/bin/mrinfo -> /home/bwgig/mrtrix3/bin/mrinfo
> 5ttgen: Loading header for image file 'input.mif'
> 5ttgen: [DEBUG] image.__init__() (from fsl.py:62): ['/home/bwgig/mrtrix3/bin/mrinfo', 'input.mif', '-json_all', '/home/bwgig/Schreibtisch/rTMS/data/180629_0946/5ttgen-tmp-3M2B1W/mrtrix-tmp-XY3Y8N.json']
> 5ttgen: [DEBUG] image.__init__() (from fsl.py:62): {'_intensity_offset': 0.0, '_format': u'MRtrix', '_transform': [[0.995126049999522, -0.0951284235521, 0.025975520107249, -81.217260721004], [0.0827279841754891, 0.94871820186333, 0.305106299652209, -150.283410323083], [-0.0536677300303433, -0.3014703243865, 0.951963979501165, -130.97506784022], [0.0, 0.0, 0.0, 1.0]], '_intensity_scale': 1.0, '_datatype': u'UInt16LE', '_name': u'input.mif', '_keyval': {u'EchoTime': u'0.00494', u'RepetitionTime': u'2.53', u'mrtrix_version': u'3.0_RC3-51-g52a2540d', u'FlipAngle': u'7', u'comments': u'VP_9 (VP_9) [MR] MPRAGE_freesurfer\nstudy: PICHT 226_TMSNAVI [ ORIGINAL PRIMARY M ND NORM ]\nDOB: 11/05/1993\nDOS: 29/06/2018 10:03:12', u'PhaseEncodingDirection': u'j-', u'TotalReadoutTime': u'0', u'command_history': u'mrconvert "/home/bwgig/Schreibtisch/rTMS Studie Melina/MRT Daten/180629_0946/003_MPRAGE_freesurfer" "t1.mif" (version=3.0_RC3-51-g52a2540d)\n/home/bwgig/mrtrix3/bin/mrconvert "/home/bwgig/Schreibtisch/rTMS/data/180629_0946/t1.mif" "/home/bwgig/Schreibtisch/rTMS/data/180629_0946/5ttgen-tmp-3M2B1W/input.mif" "-info" (version=3.0_RC3-51-g52a2540d)'}, '_size': [176, 256, 256], '_spacing': [1.0, 1.0, 1.0], '_strides': [3, -1, -2]}
> 5ttgen: [DEBUG] run.exeName() (from run.py:351): mrconvert -> mrconvert
> 5ttgen: [DEBUG] run.versionMatch() (from run.py:57): Version-matched executable for mrconvert: /home/bwgig/mrtrix3/bin/mrconvert
> 5ttgen: [DEBUG] run._shebang() (from run.py:67): File "/home/bwgig/mrtrix3/bin/mrconvert": Not a text file
> 5ttgen: [DEBUG] run.command() (from fsl.py:71): To execute: [['/home/bwgig/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 176x256x256, voxel spacing 1x1x1, datatype UInt16LE
> mrconvert: [INFO] opening image "-1,+2,+3"...
> mrconvert: [INFO] creating image "T1.nii"...
> mrconvert: [INFO] image "T1.nii" created with dimensions 176x256x256, voxel spacing 1x1x1, datatype UInt16LE
> mrconvert: [100%] copying from "input.mif" to "T1.nii"
> 5ttgen: [DEBUG] run.exeName() (from run.py:351): maskfilter -> maskfilter
> 5ttgen: [DEBUG] run.versionMatch() (from run.py:57): Version-matched executable for maskfilter: /home/bwgig/mrtrix3/bin/maskfilter
> 5ttgen: [DEBUG] run._shebang() (from run.py:67): File "/home/bwgig/mrtrix3/bin/maskfilter": Not a text file
> 5ttgen: [DEBUG] run.command() (from fsl.py:115): To execute: [['/home/bwgig/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 coordinate 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 1x1x1, datatype Float32LE
> maskfilter: [ 0%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 2%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 4%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 5%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 7%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 9%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 11%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 13%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 15%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 16%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 18%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 20%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 22%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 24%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 25%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 27%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 29%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 31%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 33%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 35%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 36%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 38%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 40%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 42%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 44%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 45%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 47%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 49%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 51%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 53%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 55%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 56%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 58%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 60%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 62%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 64%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 65%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 67%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 69%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 71%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 73%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 75%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 76%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 78%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 80%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 82%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 84%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 85%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 87%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 89%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 91%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 93%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 95%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 96%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [ 98%] uncompressing image "/usr/share/fsl/5.0/data/standa maskfilter: [100%] uncompressing image "/usr/share/fsl/5.0/data/standa 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: [ 0%] applying dilate filter to image MNI152_T1_1mm_brain maskfilter: [ 20%] applying dilate filter to image MNI152_T1_1mm_brain maskfilter: [ 40%] applying dilate filter to image MNI152_T1_1mm_brain maskfilter: [ 60%] applying dilate filter to image MNI152_T1_1mm_brain maskfilter: [ 80%] applying dilate filter to image MNI152_T1_1mm_brain 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:375): Command fsl5.0-standard_space_roi not found in MRtrix3 bin/ directory
> 5ttgen: [DEBUG] run.exeName() (from run.py:377): 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', '-roiFOV']]
> Command: fsl5.0-standard_space_roi T1.nii T1_preBET.nii.gz -maskMASK mni_mask.nii -roiFOV
> terminate called after throwing an instance of 'NEWMAT::SingularException'
> Aborted (core dumped)
> Could not open matrix file T1_preBET_tmp_to_std_inv.mat
> terminate called after throwing an instance of 'NEWMAT::IncompatibleDimensionsException'
> Aborted (core dumped)
> Cannot open volume T1_preBET_tmp_standard_mask_to_in for reading!
> Image Exception : #22 :: ERROR: Could not open image T1_preBET_tmp_standard_mask_to_in
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> Aborted (core dumped)
> Could not open matrix file T1_preBET_tmp_to_std_inv.mat
> terminate called after throwing an instance of 'NEWMAT::IncompatibleDimensionsException'
> Aborted (core dumped)
> Image Exception : #22 :: ERROR: Could not open image T1_preBET_tmp_standard_roi_to_in
> 5ttgen: [ERROR] Unable to find FSL output file for path "T1_preBET"
> 5ttgen: Changing back to original directory (/home/bwgig/Schreibtisch/rTMS/data/180629_0946)
> 5ttgen: Contents of temporary directory kept, location: /home/bwgig/Schreibtisch/rTMS/data/180629_0946/5ttgen-tmp-3M2B1W/
> bwgig@bwgchariteIG:~/Schreibtisch/rTMS/data/180629_0946$
Best, Lucius
Hi Lucius,
I suspect you don’t have exactly the same issue as above; here is the relevant section of your terminal output:
Command: fsl5.0-standard_space_roi T1.nii T1_preBET.nii.gz -maskMASK mni_mask.nii -roiFOV
terminate called after throwing an instance of 'NEWMAT::SingularException'
Even though the
5ttgen: [ERROR] Unable to find FSL output file for path "T1_preBET"
message occurs for you too, this is downstream of the fundamental issue, which is an FSL command throwing an exception due to trying to invert a non-singular matrix (or something like that). If the problem were being caused by the absence of a particular standard space image, I would expect a different error to appear within the output of standard_space_roi.
You could try breaking up the steps within the FSL standard_space_roi script to find out exactly which step is encountering the error. I suspect it would be something to do with registration: If the underlying tools can’t get a good alignment of your image to the template, then all sorts of things could potentially go wrong in subsequent steps.
Rob
Hello,
I agree with Rob. By the way, if the problem still exists, just add the files of this link to
usr/share/fsl/5.0/data/standard/
If the standard folder does not exist in this path just create it manually.
Dear Rob and Sepehr,
thanks for your answers. I guess the problem was based on conflicting versions.
It’s now working properly after:
sudo apt-get upgrade fsl-5.0-core
Hi, I also met this problem. The environment is MRtrix3 and fsl installed on my Win10’s Ubuntu subsystem (WSL).
Here is part of the -debug information:
5ttgen: [DEBUG] run.exeName() (from run.py:66): standard_space_roi -> standard_space_roi
5ttgen: [DEBUG] run.versionMatch() (from run.py:373): Command standard_space_roi not found in MRtrix3 bin/ directory
5ttgen: [DEBUG] run.exeName() (from run.py:375): standard_space_roi -> standard_space_roi
5ttgen: [DEBUG] run._shebang() (from run.py:67): File "standard_space_roi": string "#!/bin/sh": ['/bin/sh']
5ttgen: [DEBUG] run.command() (from fsl.py:120): To execute: [['/bin/sh', '/usr/local/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
/usr/local/fsl/bin/standard_space_roi: 1: /usr/local/fsl/bin/standard_space_roi: dc: not found
/usr/local/fsl/bin/standard_space_roi: 1: /usr/local/fsl/bin/standard_space_roi: dc: not found
/usr/local/fsl/bin/standard_space_roi: 1: /usr/local/fsl/bin/standard_space_roi: dc: not found
Error: no output filename specified!
Image Exception : #63 :: No image files match: T1_preBET_tmp_standard_roi
Image Exception : #22 :: Failed to read volume T1_preBET_tmp_standard_roi
Error : No image files match: T1_preBET_tmp_standard_roi
Failed to read volume T1_preBET_tmp_standard_roi
Error : No image files match: T1_preBET_tmp_standard_roi
Image Exception : #63 :: No image files match: T1_preBET_tmp_standard_roi_to_in
Image Exception : #22 :: Failed to read volume T1_preBET_tmp_standard_roi_to_in
Error : No image files match: T1_preBET_tmp_standard_roi_to_in
Failed to read volume T1_preBET_tmp_standard_roi_to_in
Error : No image files match: T1_preBET_tmp_standard_roi_to_in
5ttgen: [ERROR] Unable to find FSL output file for path "T1_preBET"
Does anyone have an idea? Thanks so much.
1 Like
Hi Berlin & welcome!
I believe this is a slightly different cause for the issue, that I only discovered fairly recently myself:
/usr/local/fsl/bin/standard_space_roi: dc: not found
“dc” is a Unix calculator program, which standard_space_roi attempts to execute without first checking for its existence in PATH. Installing it should hopefully rectify the issue for you.
I do however wonder how much of my past grievances with calling standard_space_roi in the 5ttgen fsl script have been due to the absence of this program, but were never properly identified as such…
4 Likes
Thank you so much Smith. I’m relatively new to Linux and you pointed out the key part of the debug message that I didn’t understand.
sudo apt-get install dc did resolved the problem I encountered.
Many thanks again. 
2 Likes
I have the same error message:
[ERROR] Unable to find FSL output file for path “T1_preBET”
when I used option -nocrop. However, it works fine without that -nocrop option.
Can anybody here help me to solve the problem. Thank you.
Hi @xingzhe,
I don’t immediately see why use of the -nocrop option would affect this particular issue: whether or not the FSL command standard_space_roi is executed depends on whether or not the input T1 image is either “pre-masked” (-premnasked option), or an explicit brain mask image is provided via the -mask option, but whether or not the final generated image is cropped should not influence this area of the code.
Have you tried installing the dc command? This is the only diagnosis I have been able to make for this specific error thus far.
Rob
Hi Rob! Thank you very much for your help. Eventually I had to use a detour to solve the -nocrop problem. I manipulated T1 image, so I didn’t need to use -nocrop anymore. I have dc command in my computer. xingzhe.
To add to the list of possible root causes:
In my case, my FSL installation was missing the imcp executable, which is called in standard_space_roi.
These were my 5ttgen debug logs:
Command: standard_space_roi T1.nii T1_preBET.nii.gz -maskMASK mni_mask.nii -roiNONE
/opt/fsl/bin/standard_space_roi: 241: /opt/fsl/bin/standard_space_roi: /opt/fsl/bin/imcp: not found
5ttgen: [ERROR] Unable to find FSL output file for path "T1_preBET"
The issue was fixed by running the script fslpython_install.sh, as described in the FSL docs: FslInstallation - FslWiki
For context: I was running MRtrix 3.0_RC3 with FSL 6.0.0 in a Docker container. The Dockerfile for the image was generated using Neurodocker 0.7.0. In this version of Neurodocker, a bug (then fixed in 0.8.0, see #378) caused the omission of the instruction to run the fslpython_install.sh script.