New subject: A Question about How to Map Parcels of the Cortex on the surface of the Brain Cortex

12 May 2019

      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:
...
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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:
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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:
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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

Re: [Freesurfer] A Question about How to Map Parcels of the Cortex on the surface of the Brain Cortex