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





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
>
>
>
>
>