I’m having trouble with step one of userdocs.mrtrix.org/en/latest/tutorials/hcp_conectome.html, and I don’t get as far as what is discussed at 5ttgen. What’s wrong below?
fred@fred-VirtualBox:~/Downloads/100307$ find . -name *restore_brain* -print
./MNINonLinear/T1w_restore_brain.nii.gz
./MNINonLinear/T2w_restore_brain.nii.gz
./T1w/T1w_acpc_dc_restore_brain.nii.gz
./T1w/T2w_acpc_dc_restore_brain.nii.gz
fred@fred-VirtualBox:~/Downloads/100307$ 5ttgen fsl T1w/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. Please consult the help page (-help option) for more information.
5ttgen:
5ttgen: Generated temporary directory: /tmp/5ttgen-tmp-PNE2X7/
Command: mrconvert T1w/T1w_acpc_dc_restore_brain.nii.gz /tmp/5ttgen-tmp-PNE2X7/input.mif -quiet
Segmentation fault (core dumped)
5ttgen: [ERROR] Command failed: mrconvert T1w/T1w_acpc_dc_restore_brain.nii.gz /tmp/5ttgen-tmp-PNE2X7/input.mif -quiet
5ttgen: Changing back to original directory (/home/fred/Downloads/100307)
5ttgen: Deleting temporary directory /tmp/5ttgen-tmp-PNE2X7/
fred@fred-VirtualBox:~/Downloads/100307$ 5ttgen fsl MNINonLinear/T1w_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. Please consult the help page (-help option) for more information.
5ttgen:
5ttgen: Generated temporary directory: /tmp/5ttgen-tmp-TNDBRT/
Command: mrconvert MNINonLinear/T1w_restore_brain.nii.gz /tmp/5ttgen-tmp-TNDBRT/input.mif -quiet
Segmentation fault (core dumped)
5ttgen: [ERROR] Command failed: mrconvert MNINonLinear/T1w_restore_brain.nii.gz /tmp/5ttgen-tmp-TNDBRT/input.mif -quiet
5ttgen: Changing back to original directory (/home/fred/Downloads/100307)
5ttgen: Deleting temporary directory /tmp/5ttgen-tmp-TNDBRT/