Greetings Freesurfer Gurus,
I'm having a little trouble with a small minority of my subjects whereby dura
is being classed as cortical surface . I've played around with gcut and the
watershed parameters, but have so far been unable to achieve a satisfactory
cleanup. Before I give up and invest some time and effort in performing manual
edits, I thought I would see if I could achieve a better result using software
external to freesurfer. This is my current approach:
run the full recon-all pipeline.
Use mri_convert to transform the resulting T1.mgz into nifti format
Apply skullstripping (in this case, a combination of SPM segmentations
and erosion/dilation operations, which seems to work quite well on our data)
Use mri_convert to convert the skullstripped T1 back to .mgz format
Replace the original 'brainmask.mgz' with the newly generated image.
Regenerate the cortical surface, using the new brainmask file:
'recon-all -autorecon-pial -subjid {subect}'
I would very much like to know if this is a valid procedure, and if any steps
prior to the cortical surface regeneration also need to be re-run with this new
mask in order to produce valid measures. I'm (perhaps naively) assuming that
all subcortical images/measures won't be affected (except for the cortical
ribbon in the aseg.mgz, but as I understand it that's not really used for
anything?)
I've seen various hints in other forum posts that people have experimented with
using FSL's bet tool for brainmask cleanup, but I haven't seen any guidance on
the exact steps for doing this.
Final point: I've made sure to check that the newly created brainmask.mgz lines
up with the other freesurfer outputs in Freeview without any left/right
flipping. This should be enough to ensure I haven't messed up the orientation
info in the mgz/nii conversion process, right?
Best wishes,
Richard
Richard Parker
Postgraduate Research Student
Maurice Wohl Clinical Neuroscience Institute
King's College London
Telephone: 07943515208
Email: richard.r.par...@kcl.ac.uk
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