ERROR in 5ttgen fsl：only 5 of 10 structures were segmented successfully

[NicDC]

Dear @SAA ,

There’s a number of posts related to this issue, maybe one of them can help you?

5ttgen fsl issues

FIRST failure The following error messages have frequently been observed from the 5ttgen fsl script: FSL FIRST has failed; not all structures were segmented successfully Waiting for creation of new file "first-L_Accu_first.vtk" FSL FIRST job has been submitted to SGE; awaiting completion (note however that FIRST may fail silently, and hence this script may hang indefinitely) Error messages that may be found in the log files within the script’s temporary directory include: Cannot open volume f…

5ttgen fsl ERROR: only 0 of 10 structures were segmented successfully

Hi all, I am trying to follow the ISMRM tutorial to create a tissue-segmented image using the Human Connectome data. However, the first step 5ttgen fsl stuck at run_first_all command and gave me an error message below: yukai@yukai-Oryx-Pro:~/HCP/20180121_MRtrix3/test_5ttgen$ 5ttgen fsl T1w_acpc_dc_restore_brain.nii.gz 5TT.mif -premasked 5ttgen: 5ttgen: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. …

5ttgen - run first all error

Hi all, I have recently started to work on MRtrix and I am getting the error below when I try to run 5ttgen fsl T1.mif 5tt_nocoreg.mif. I checked previous posts and errors, I have all standard files error and my error files in first.logs folder are empty. So I am not sure what causes the error, I would appreciate any help or suggestions a lot 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.…

All the best,
Nick