5ttgen gives error in mrtrix reconstruction

[akelkar26]

Hi,

5ttgen gives an error when I run qsiprep 0.13.0RC1 on my data. It runs for all other subjects but errors on this one.

Here is my command:

screen docker run -ti \ -v /Users/neurouser1/Documents/TMS_Aphasia/bids_directory/:/data \ -v /Users/neurouser1/Documents/TMS_Aphasia/qsiprep_detdsistudio/:/out \ -v /Users/neurouser1/Documents/fs_files/:/license \ -v /Users/neurouser1/Documents/TMS_Aphasia/scratch/:/scratch \ -v /Users/neurouser1/Documents/TMS_Aphasia/qsiprepout_dwionly/qsiprep/:/recon_input \ pennbbl/qsiprep:0.13.0RC1 \ /data /out participant \ --participant_label sub-TMSA59 \ --recon_input /recon_input/ \ --recon_only \ --recon_spec dsi_studio_gqi \ --fs-license-file /license/license.txt \ -w /scratch/ \ --output-resolution 1.3 \ --n_cpus 15 \ --omp-nthreads 8 \ --mem_mb 150000 \

Here is my error:

5ttgen: Changing to temporary directory (/scratch/qsirecon_wf/sub-TMSA59_mrtrix_multishell_msmt/anat_ingress_wf/create_5tt/5ttgen-tmp-P7Q2VB/) 5ttgen: [WARNING] Voxel size larger than expected for T1-weighted images ([1.3, 1.3, 1.3]); note that ACT does not require re-gridding of T1 image to DWI space, and indeed retaining the original higher resolution of the T1 image is prefe rable Command: mrconvert input.mif T1.nii -strides -1,+2,+3 Command: mrcalc T1.nii mask.mif -mult T1_masked.nii.gz Command: fast T1_masked.nii.gz 5ttgen: [WARNING] Generating 1mm isotropic T1 image for FIRST in hope of preventing failure, since input image is of lower resolution Command: mrresize T1.nii T1_1mm.nii -voxel 1.0 -interp sinc 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_1mm.nii -o first 5ttgen: [ERROR] FSL FIRST has failed; only 8 of 10 structures were segmented successfully (check /scratch/qsirecon_wf/sub-TMSA59_mrtrix_multishell_msmt/anat_ingress_wf/create_5tt/5ttgen-tmp-P7Q2VB/first.logs) 5ttgen: Changing back to original directory (/scratch/qsirecon_wf/sub-TMSA59_mrtrix_multishell_msmt/anat_ingress_wf/create_5tt) 5ttgen: Contents of temporary directory kept, location: /scratch/qsirecon_wf/sub-TMSA59_mrtrix_multishell_msmt/anat_ingress_wf/create_5tt/5ttgen-tmp-P7Q2VB/ Return code: 1

Could you please advise?

Thank you Best, Apoorva