Hi all, I’m using 5ttgen fsl on a T1 to DWI registered image and it’s stuck on Waiting for creation of new file "first-L_Accu_first.vtk". I checked the first.logs with cat * . logs/*.e*: Cannot open volume first-L_Accu_corr for reading! Cannot open volume first-L_Accu_first for reading! Image E…

Hi Amir, I have encountered a similar issue, fsl first has actually failed to segment the L Accumbens. I haven’t actually tried to solve this issue, but must ask two questions first: Are you using a MPRAGE or MP2RAGE T1-image as input into 5ttgen?. Only the MP2RAGE is problematic for me. Doe…

Hi Alistair, 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?. Interestingly it’s running smoothly on native T1 image. I think the registration was problematic. But a further problem ari…

All other first.vtks like Thal, Put, etc are built. OK, that’s interesting; I was under the impression that it was most typically the registration steps in run_first_all that failed, in which case none of the segmentations would be produced. Firstly, I would confirm that you are able to reproduc…

Thanks Robert. [image] rsmith: Firstly, I would confirm that you are able to reproduce the fault by manually executing run_first_all on the relevant T1 image. It may seem like a pointless exercise, but from a software support perspective it makes a very big difference whether MRtrix3 is doing s…

I manually ran run_first_all and it completed without error, but there’s the same error in the logs, it can not generate L-accu. It seems the problem is because of the registration, since it runs without any error on native T1 brain. Depends on your definition of “completed without error”. As far…

Hey @rsmith , @AmirHussein , Ill weigh in with the co-registrations question: [image] AmirHussein: Can I do the registration after 5ttgen? My preference is to do the co-registration after, as the tissue-segmentation software is already highly-sensitive to different scanners, acquisition types…

I think that there is no need to do any interpolation / resampling to lower resolution in coregistration. It absolutely suffices for mrtrix processing only to modify the vox2ras transform in the image header of either T1 or DWI. This operation is absolutely safe and therefore can be done before or a…

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5ttgen stuck at first-L_accu_first.vtk

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