Dear MRtrix3 team,
I’m trying to run the 5ttgen command to conduct tissue segmentation in preparation for Anatomically Constrained Tractography (ACT). I encounter the following error when I try to do this:
$ 5ttgen fsl T1.coreg.nii 5tt_act.mif 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: Generated temporary directory: /ibscratch/users/uqisaham/CAI_imaging/files_relevant_to_analysis/mrtrix3_Preprocessed_Data/C_S01_PZ_3T/HARDI/5ttgen-tmp-I8AC9V/ Command: mrconvert /ibscratch/users/uqisaham/CAI_imaging/files_relevant_to_analysis/mrtrix3_Preprocessed_Data/C_S01_PZ_3T/HARDI/T1.coreg.nii /ibscratch/users/uqisaham/CAI_imaging/files_relevant_to_analysis/mrtrix3_Preprocessed_Data/C_S01_PZ_3T/HARDI/5ttgen-tmp-I8AC9V/input.mif 5ttgen: Changing to temporary directory (/ibscratch/users/uqisaham/CAI_imaging/files_relevant_to_analysis/mrtrix3_Preprocessed_Data/C_S01_PZ_3T/HARDI/5ttgen-tmp-I8AC9V/) Command: mrconvert input.mif T1.nii -stride -1,+2,+3 Command: maskfilter /clusterdata/apps/fsl/data/standard/MNI152_T1_1mm_brain_mask_dil.nii.gz dilate mni_mask.nii -npass 4 Command: standard_space_roi T1.nii T1_preBET.nii.gz -maskMASK mni_mask.nii -roiFOV Command: bet T1_preBET.nii.gz T1_BET.nii.gz -f 0.15 -R Command: fast T1_BET.nii.gz Command: run_first_all -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 5ttgen: **5ttgen: [ERROR] Command failed: run_first_all -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 (fsl.py:168)** 5ttgen: Output of failed command: The command you have requested cannot be found or is not executable Unable to run job: denied: host "compute-0-0.local" is no submit host. Exiting. 5ttgen: Changing back to original directory (/ibscratch/users/uqisaham/CAI_imaging/files_relevant_to_analysis/mrtrix3_Preprocessed_Data/C_S01_PZ_3T/HARDI) 5ttgen: Script failed while executing the command: run_first_all -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 5ttgen: For debugging, inspect contents of temporary directory: /ibscratch/users/uqisaham/CAI_imaging/files_relevant_to_analysis/mrtrix3_Preprocessed_Data/C_S01_PZ_3T/HARDI/5ttgen-tmp-I8AC9V/
The input image is the recommended T1-weighted image co-registered to the diffusion imaging series as per the instructions here: http://mrtrix.readthedocs.io/en/latest/quantitative_structural_connectivity/act.html.
Initially I thought that the issue had something to do with path definition to FSL on our computers but this is not the case. FSL is working correctly and I was informed that it was recently updated on our computers.
Our IT team have asked that I contact you about this issue. I can’t run this command on head node so any suggestions to resolve this issue would be appreciated!
EDIT (04/09/2017): Another researcher at my institute has encountered the same error.