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Dear Manoj,
in case you want to rely on tools provided with FreeSurfer only, N3 can produce
good results even for 7T data. However, in my experience, you need to supply a
brainmask to N3 to achieve very similar results compared to SPM. Otherwise,
especially around the temporal lobes the inhomogeneity will not be corrected
sufficiently.
Tweaking recon-all for this is possible, but is slightly more complicated than
changing the parameters of mri_nu_correct only. Furthermore, the procedure may
change in case you use higher resolution 7T data.
Apart from that SPM, N3 as well as N4 of ANTs (also using a brainmask) will all
produce similar results. I mostly use SPM for pre-processing my 7T data as it
is the easiest to use in my processing pipeline.
Best,
Falk
________________________________
Von: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Manoj Saranathan
<manoj...@radiology.arizona.edu>
Gesendet: Montag, 6. Januar 2020 23:51:23
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Freesurfer 7T MPRAGE
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Hi,
I am trying to process 7T MPRAGE data (not MP2RAGE) using recon-all. In
previous threads, a few people have suggested using SPM to correct for bias
first and then running recon-all. Alternatively I saw a thread which suggests
modifying the mri_nu_correct command
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg61913.html
Can I edit the recon-all to run this alternative command and simply run
recon-all? The threads are all really old and SPM is now SPM12 which
integrates things. Is this modified bias correction inside FS as good as SPM ?
I am mainly interested in thalamic segmentation.
Are there others with the same issue?
Thanks
manoj
Manoj Saranathan
Associate Professor, Dept. of Medical Imaging
University of Arizona
Ph: 520-626-6531
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