5ttgen fsl removing part of the brain

Hi all

I’m very new to MRTrix and I’m trying to follow the BATMAN tutorial on HCP data. The structural data was preprocessed by the HCP consortium. However, when running 5ttgen fsl T1_raw.mif 5tt_nocoreg.mif, I got the following error

5ttgen: [WARNING] Generated image does not perfectly conform to 5TT format:
5ttgen: [WARNING] 5ttcheck: [WARNING] Image "result.mif" contains 27 brain voxels with non-unity sum of partial volume fractions
5ttgen: [WARNING] 5ttcheck: [WARNING] Input image does not perfectly conform to 5TT format, but may still be applicable (suggest re-running using the -masks option to see voxels where tissue fractions do not sum to 1.0)

I’ve understood from other threads that this might not be the end of the world, but inspecting the data shows that big parts of the brain is gone:

I used mrconvert T1w_acpc_dc_restore_brain.nii.gz T1_raw.mif to create the the T1_raw.mif and this looks like perfectly fine.

Best regards and thanks for any help,
Karin

Hi all:

The problem resolved it self by running 5ttgen fsl T1w_acpc_dc_restore_brain.nii.gz 5TT.mif -premasked instead. (Posting if someone encounters the same error)

Best
Karin

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