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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"
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"
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Maedeh Khalilian