Hi Maedeh
in principle you can, although it would be a lot easier if you just had a
reasonable quality T1. If not, you will need to create all the files that
recon-all expects to exist prior to the topology correction step (wm.mgz,
norm.mgz, orig.mgz, ....). Maybe the easiest thing to do would be to use
your gray/white/csf segmentation to create a synthetic T1 volume? Set all
the wm voxels to 110, all the gray to 70 and all the csf to 20, or
something like that?
cheers
Bruce
On Thu, 11 Jul 2019, Maedeh Khalilian wrote:
External Email - Use Caution
From: "Maedeh Khalilian" <m.khalil...@sutech.ac.ir>
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Date: Thu, 11 Jul 2019 07:37:05 +0430
Subject: A Question Regarding Topology Correction
Dear FreeSurfer experts,
I know that FreeSurfer does segmentation, surface reconstruction and topology
correction through
its routine pipeline using "recon-all" . However, I have some T2w brain MR
images and I have done
the segmentation and extracted WM, GM, and CSF with my own algorithm. Now I
need to remove back to
back (i.e. a part of topology correction) which is caused in sulci due to the
segmentation. In
other word, after doing my segmentation, I wanna open the closed concavities in
CSF that were open
originally.
Now I wanna know if I can do the topology correction using FreeSurfer while I
have done the
segmentation by myself? I would be grateful if you could help me with that.
Best,
Maedeh
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