Hi Maedeh
there are a bunch of steps involved in the topology correction that you
will need to run (e.g. surface inflation, quasi-homeomorphic spherical
mapping, etc...). If you can synthesize a T1-ish image you can just run it
through recon-all and it should do the right thing. Otherwise you can look
at the recon-all.cmd from one of our example subjects such as bert and see
what needs to be run post-segmentation, but there are some T1-weighted
assumptions in various places
cheers
Bruce
On Mon, 5 Aug 2019, Maedeh Khalilian wrote:
External Email - Use Caution
Dear Bruce,
The other day I asked you about doing topology correction on my own
segmentation(I have put my first e-mail and you response in the following
so u can track easier). according to what you suggested, I have created a
synthetic T1 volume based on my own segmentation. Now I wonder what to do
exactly as the second step. Should I use "mris_fix_topology"?
I would be grateful if you could help me with that.
Best,
Maedeh
"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
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"
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