I am having the 5ttgen error: FSL FIRST has failed.
5ttgen fsl T1_raw.mif 5tt_nocoreg.mif -premasked
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 scratch directory: /home/nas/shahzad/ADF/ADNI/MRTrix_Preprocessing/13031/013_S_6970/DTI/5ttgen-tmp-MSOX8R/
Command: mrconvert /home/nas/shahzad/ADF/ADNI/MRTrix_Preprocessing/13031/013_S_6970/DTI/T1_raw.mif /home/nas/shahzad/ADF/ADNI/MRTrix_Preprocessing/13031/013_S_6970/DTI/5ttgen-tmp-MSOX8R/input.mif
5ttgen: Changing to scratch directory (/home/nas/shahzad/ADF/ADNI/MRTrix_Preprocessing/13031/013_S_6970/DTI/5ttgen-tmp-MSOX8R/)
Command: mrconvert input.mif T1.nii -strides -1,+2,+3
Command: fast T1.nii
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 -b
5ttgen: [ERROR] FSL FIRST has failed; only 6 of 10 structures were segmented successfully (check /home/nas/shahzad/ADF/ADNI/MRTrix_Preprocessing/13031/013_S_6970/DTI/5ttgen-tmp-MSOX8R/first.logs)
5ttgen: Scratch directory retained; location: /home/nas/shahzad/ADF/ADNI/MRTrix_Preprocessing/13031/013_S_6970/DTI/5ttgen-tmp-MSOX8R/
I am pasting here the contents of first.. files:
first.e*.*
/opt/fsl/bin/run_first: 1: bc: not found
/opt/fsl/bin/run_first: 1: bc: not found
/opt/fsl/bin/run_first: 1: bc: not found
/opt/fsl/bin/run_first: 1: bc: not found
/opt/fsl/bin/run_first: 1: bc: not found
/opt/fsl/bin/run_first: 141: [: -ne: unexpected operator
WARNING: NO INTERIOR VOXELS TO ESTIMATE MODE
first.e*.*
/opt/fsl/bin/run_first: 1: bc: not found
/opt/fsl/bin/run_first: 1: bc: not found
/opt/fsl/bin/run_first: 1: bc: not found
/opt/fsl/bin/run_first: 1: bc: not found
/opt/fsl/bin/run_first: 1: bc: not found
/opt/fsl/bin/run_first: 141: [: -ne: unexpected operator
WARNING: NO INTERIOR VOXELS TO ESTIMATE MODE
first.o*.*
create shapeModel
done creating shapeModel
0.114377 -0.0311928 -1.82781
1.53285 0.494281 0.114203
0.667625 -1.72792 -0.0184571
NEw done imodes transform
Error: cannot find image first-L_Accu_first
first.o*.*
create shapeModel
done creating shapeModel
0.114377 -0.0311928 -1.82781
1.53285 0.494281 0.114203
0.667625 -1.72792 -0.0184571
NEw done imodes transform
Error: cannot find image first-R_Accu_first
first.o*.*
create shapeModel
done creating shapeModel
create shapeModel
done creating shapeModel
0.114377 -0.0311928 -1.82781
1.53285 0.494281 0.114203
0.667625 -1.72792 -0.0184571
NEw done imodes transform
done registering model
mode 16.9676
0.114377 -0.0311928 -1.82781
1.53285 0.494281 0.114203
0.667625 -1.72792 -0.0184571
NEw done imodes transform
D
336 3204 3204 336
open file first-R_Caud_first.vtk to save.
succesfully opened file first-R_Caud_first.vtk to save.
first.o*.*
create shapeModel
done creating shapeModel
0.114377 -0.0311928 -1.82781
1.53285 0.494281 0.114203
0.667625 -1.72792 -0.0184571
NEw done imodes transform
Error: cannot find image first-L_Puta_first
first.o*.*
create shapeModel
done creating shapeModel
0.114377 -0.0311928 -1.82781
1.53285 0.494281 0.114203
0.667625 -1.72792 -0.0184571
NEw done imodes transform
Error: cannot find image first-R_Puta_first
first_post.e*.*
Image Exception : #63 :: No image files match: first-L_Accu_corr
terminate called after throwing an instance of ‘std::runtime_error’
what(): No image files match: first-L_Accu_corr
Aborted (core dumped)
Image Exception : #63 :: No image files match: first-L_Accu_first
terminate called after throwing an instance of ‘std::runtime_error’
what(): No image files match: first-L_Accu_first
Aborted (core dumped)
Image Exception : #63 :: No image files match: first_all_none_origsegs
Image Exception : #22 :: Failed to read volume first_all_none_origsegs
Error : No image files match: first_all_none_origsegs
Failed to read volume first_all_none_origsegs
Error : No image files match: first_all_none_origsegs
first_post.o*.*