Thanks a lot for your reply Doug.
I will re-do my recon as you said. 
Do you think the "blurriness" might be because of inadequate inflating of the surface? My expert option file was : mris_inflate -n 15 -w 10.
In addition to your recommendations, do you think I need to increase "n"?

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 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Wednesday, December 11, 2019 7:04 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] flat maps in native space
 
I'm not sure what is going on here, but I would guess that the v6 hires
stream is not behaving  very well. I would suggest using a patch I
created the HCP. If you are in the version 6 environment, you can run
recon-all.v6.hires the same way you did recon-all, but do not use -hires
and instead use -conf2hires

doug


On 12/9/19 6:17 PM, Nasiriavanaki, Zahra wrote:
> 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
> >
> >
> >
> >
> >
>
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