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 :four_leaf_clover:

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 -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
5ttgen: [ERROR] FSL FIRST has failed; only 0 of 10 structures were segmented successfully (check /cubric/data/c1958866/Diff_proc/update/sub_03_volumes/5ttgen-tmp-DU4LWC/first.logs)

Many thanks in advance!

Welcome Ozge!

In the absence of any information at all in log files, I’m really limited in capacity to diagnose…

  1. The first barrier is the fact that it’s an FSL command that is (supposedly) failing. It happens to be being invoked from within an MRtrix3 wrapper, so the first diagnosis step is to separate the two. Take an image for which executing run_first_all should be possible, isolate it from any and all references to MRtrix3, and execute run_first_all as a standalone command.

  2. run_first_all is being executed on the input T1-weighted image. I know that T1-weighted images that include a lot of spinal column can be problematic for FSL’s bet tool; that’s why the standard_space_roi command is called beforehand. So you could try executing run_first_all on image T1_preBET.nii.gz instead? The other alternative is to run it on image T1_BET.nii.gz, and provide the -b option to run_first_all.

  3. Also, if you’re providing 5ttgen fsl with an image that has already been skull-stripped, but are not specifying the -premasked option, that could conceivably lead to issues here (and the results of bet would likely look pretty ordinary in this case also).

Good luck!

Hi @rsmith,

Many thanks for your reply. I guess it was due to FSL command failing, I used an in-house MATLAB implementation including the analysis and it is working alright. I still tried the options you provided but run_first_all did not work individually. I will update if I can achieve to run 5ttgen fsl by itself later. However, it is all good for me now and thanks a lot for your time and response!