5ttgen stuck at first-L_accu_first.vtk

3

Hi Alistair,

  1. All images are acquired on a 3T Siemens TimTrio scanner and dicom header says the T1 is t1_mpr_ns_sag_p2_iso. I guess this means MPRAGE, not MP2RAGE, right?.

  2. Interestingly it’s running smoothly on native T1 image. I think the registration was problematic. But a further problem arises: Is it possible to register after 5ttgen?
    For more info, to perform the registration I converted biasfield corrected preprocessed dwi into nifti, extract the first b0, and use fsl flirt (cost function=mutualinfo, dof=12). Couldn’t do it by mrregister, the command is not suitable for such conversions.

Bests,
Amir

Update: 5ttgen has finished with this error:

5ttgen: [WARNING] Command failed: 5ttcheck result.mif
5ttgen: [WARNING] Generated image does not perfectly conform to 5TT format