Dear Freesurfer experts
Hi
I have a follow up question regarding the flat maps in native space. I was trying to re-do the "making cuts and flattening the maps" step, but first I want to know if these individual maps looks ok to you. As you see in some parts of the brain the suci and gyri are blurred and this causes some of the cuts (the cut in Calcarine fissure) to be distorted (image attached). I'm not sure if this is normal to see the blurriness and distorted shape of the brain in individual maps or not. Is it possible that reconstruction hasn't been done well and that's causing this problem?
Thanks a lot Mona
[cid:2a21516c-7739-4738-8794-aeff9cf4de5b]
Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
________________________________ From: Nasiriavanaki, Zahra ZNASIRIAVANAKI@mgh.harvard.edu Sent: Friday, November 8, 2019 12:19 PM To: Bruce Fischl fischl@nmr.mgh.harvard.edu; Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] flat maps in native space
Hi Bruce
Thanks for your reply. Well, two of my subjects have this problem. I have two subjects with correct flattened maps and for 3 other subjects "the mris_flatten" is still running. I attached the directory and I would appreciate if you could please take a look.
Thanks MOna
Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Friday, November 8, 2019 11:54 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] flat maps in native space
Hi Mona
that is pretty strange looking. Is the data somewhere local that we can take a look at it? I would guess that one of the cuts left a connection around, but would need to look at it to tell. Have you flattened other subjects successfully?
cheers Bruce
On Fri, 8 Nov 2019, Nasiriavanaki, Zahra wrote:
Hi Freesurfer experts
I was trying to make flat maps for individual subjects, following instruction in https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch. For some of my subjects, the flat maps are distorted (attached image). Please let me know what you think.
Thanks Mona
[IMAGE]
Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
