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:

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From: "Maedeh Khalilian" M.Khalilian@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