5ttgen error - fsl script 'standard_space_roi'

1

Dear Experts,

I found the following issue with 5ttgen:

Command: standard_space_roi T1.nii T1_preBET.nii.gz -maskMASK mni_mask.nii -roiFOV
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] bet T1.nii T1_BET.nii.gz -f 0.15 -R (fsl.py:157)
5ttgen: [ERROR] Information from failed command:
5ttgen:
/usr/local/fsl/bin/bet failed during command:T1.nii T1_BET.nii.gz -f 0.15 -R

    Fatal error: cannot open file: -
        Function: (main)

5ttgen:
5ttgen: [ERROR] For debugging, inspect contents of scratch directory: /Volumes/DCF_1tb/Processamento/Projects/Connectome_article2/P004_2/5ttgen-tmp-34UWFG/
5ttgen: Scratch directory retained; location: /Volumes/DCF_1tb/Processamento/Projects/Connectome_article2/P004_2/5ttgen-tmp-34UWFG/
(base) MacBook-Pro-de-Diego:P004_2 diego$

I am not sure what happened.
I really appreciate any help you can provide!
Diego

1 Like
2

Hi, I can currently reproduce the same error with FSL 6.0.6 and MRtrix 3.0.3-141-g8b787e53 on macOS Ventura 13.0.1.

maskfilter: [ 20%] 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.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 “#!/usr/bin/env bash”: [‘/usr/bin/env’, ‘bash’]
5ttgen: [DEBUG] run.command() (from fsl.py:143): To execute: [[‘/usr/bin/env’, ‘bash’, ‘/Users/luciusfekonja/fsl/share/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
Fatal error: cannot open file: -
Function: (main)

      Fatal error: cannot open file: -
          Function: (main)


      Fatal error: cannot open file: -
          Function: (main)

      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: [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 “#!/usr/bin/env bash”: [‘/usr/bin/env’, ‘bash’]
5ttgen: [DEBUG] run.command() (from fsl.py:157): To execute: [[‘/usr/bin/env’, ‘bash’, ‘/Users/luciusfekonja/fsl/share/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

      Fatal error: cannot open file: -
          Function: (main)

5ttgen: [ERROR] bet T1.nii T1_BET.nii.gz -f 0.15 -R (fsl.py:157)
5ttgen: [ERROR] Information from failed command:
5ttgen:
/Users/luciusfekonja/fsl/bin/bet failed during command:T1.nii T1_BET.nii.gz -f 0.15 -R

    Fatal error: cannot open file: -
        Function: (main)

5ttgen:
5ttgen: [ERROR] For debugging, inspect contents of scratch directory: