You can fix the defect by hand. It is probably the cerebellum that is hanging on https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev...
On 3/10/2020 2:53 PM, Abraham Y wrote:
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Dear FreeSurfer developers,
I'm trying to apply Fujimoto's pipeline to reconstruct surfaces of MP2RAGE structural images. Citation: John R.Giudicessi, BA.Michael J.Ackerman., 2013. (2008). NIH Public Access. Bone, 23(1), 1–7. https://doi.org/10.1038/jid.2014.371
The MP2RAGE sequence generates several images: a UNI or flat image (T1w but with amplified noise outside the brain), a proton density image, and other images.
To be able to run freesurfer on the flat image, Fujimoto invokes freesurfer two times and then stops them immediately after the brain masking step: the primary stream (input: the flat image) and the secondary stream (the multiplicative product of the flat image and the proton density, which removes the noise). Then, the brain mask generated during the primary stream is replace by the mask generated during the secondary stream, and the primary stream is resumed. I implemented this as follows:
- run 'recon-all -s X -i Y -autorecon1' for the primary and secondary
streams
- copy the brainmask.mgz file of the secondary stream to the primary
stream (and replace the file)
- resume the primary stream with 'recon-all -s X -autorecon2 -autorecon3)
The problem with this last step is that it gets stuck at correcting defects (eg: CORRECTING DEFECT 0). Sometimes it adds "Xl defect detected". Each of these corrections takes several days to run and this is not practical for our research.
Any ideas on how I could fix this? I have attached a recon-all.log file (I stopped the process because it takes too long).
FS version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c OS: Ubuntu 18.04.2 LTS
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