From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
To: Mahshid Fouladivanda <M.Fouladivanda@sutech.ac.ir>
Cc: freesurfer@nmr.mgh.harvard.edu, "DGREVE@mgh.harvard.edu" <DGREVE@mgh.harvard.edu>
Date: Sun, 12 May 2019 10:47:23 -0400 (EDT)
Subject: Re: [Freesurfer] A Question about How to Map Parcels of the    Cortex on the surface of the Brain Cortex
 

Hi Mahshid

you can't sample cerebellar or brainstem labels onto the cortical surface
as it only represents cerebral cortex. You could create tessellations for
either of them using mri_mc or mri_tessellate. You can sample your
cortical labels to surface-based label files using mri_vol2label or to
annotations using mris_sample_parc.

cheers
Bruce
On Sun, 12 May 2019, Mahshid
Fouladivanda wrote:

>
>         External Email - Use Caution        
>
>  
> Hi,
>  
> Thanks again, for your helpful reply. The parcellation file is .nii (not extracted from Freesurfer
> but in T1 space) and the surface is .pial (extracted from free surfer). 
> By the way, the parcellation included cerebellum and brain stem which there are not in the output
> of the Freesurfer surfaces! Is it possible to keep up the cerebellum and brain stem while creating
> pial surface in Freesurfer?
> Thanks a lot.
>  
> Regards,
> Mahshid
>  
>  
>  
> From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> To: Mahshid Fouladivanda <M.Fouladivanda@sutech.ac.ir>
> Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>, DGREVE@mgh.harvard.edu
> Date: Sat, 11 May 2019 14:47:48 -0400 (EDT)
> Subject: Re: [Freesurfer] A Question about How to Map Parcels of the    Cortex on the surface of
> the Brain Cortex
> Hi Mashid
>
> We don't resample to a template space. Everything is in one native
> coordinate system or another (not quite the original scanner coords, but
> close). You can register based on just the image header, but without
> knowing more about your data and what format it is stored in I don't
> think we can help
>
> cheers
> Bruce
> On Sat, 11 May 2019, Mahshid Fouladivanda wrote:
>
> >
> >         External Email - Use Caution        
> >
> > Dear Prof. Fichl and Prof. Douglas
> >  
> > Thanks for your replay. 
> > By the way, My parcels have not been extracted from Freesurfer by using "recon-all". While, the
> > command "mri_vol2surf" needs registration file as input. Still, is it possible to use the
> mentioned
> > command?? If yes, so what about the registration information? I think that registration file
> > extracted from tkregister or etc, is for registering the output of the recon-all between the
> native
> > space and Freesurfer template space. However, my parcels are not from Freesurfer. I don't know
> > maybe I think wrong! I would be grateful by receiving your help.
> >  
> > Regards,
> > Mashid
> >  
> > Date: Fri, 10 May 2019 18:58:40 +0000
> > From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
> > Subject: Re: [Freesurfer] A Question about How to Map Parcels of the
> >    Cortex on the surface of the Brain Cortex
> > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> > Message-ID: <d2312cef-2e80-2690-501e-83895bd26dad@mgh.harvard.edu>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Are the parcels in the volume or on the surface? If in the volume, then use mri_vol2surf to map
> > them (as a "segmentation") onto the surface, then use mris_seg2annot to create an annotation
> file.
> > Run either with --help to get docs and examples
> >
> > On 5/10/2019 2:26 PM, Bruce Fischl wrote:
> > Hi Mahsid
> >
> > matlab is probably the easiest way, but without knowing what format you have them in it isn't
> easy
> > for us to say. In matlab you can use write_annotation or write_ascii_curv or something to get it
> > into a format we can handle
> >
> > cheers
> > Bruce
> >
> >
> > cheers
> > Bruce
> > On Fri, 10 May 2019, mahshid fouladivand wrote:
> >
> >
> >         External Email - Use Caution
> >
> > Hello Dear Freesurfer Experts,
> >
> > I have a high resolution brain cortex parcellation that is not extracted from Freesurfer. Now I
> > want to display the nodes(each parcels) on the pial and inflated surfaces. Both pial and inflated
> > surfaces have been extracted from T1mprage image of the corresponding subject using recon-all.
> > Also, the parcels and the T1 image are in the same space. Now, I am wondering is it possible to
> map
> > these parcels on the Freesurfer pial/inflated surface?
> > By the way, How can I create an .annot file for my parcels?
> > If you could help me with this, I really appreciate your help.
> >
> > Regards,
> > Mahshid
> >
> >  
> >
> >
>
>