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 <[email protected]>
To: Mahshid Fouladivanda <[email protected]>
Cc: "[email protected]" <[email protected]>,
[email protected]
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." <[email protected]>
> Subject: Re: [Freesurfer] A Question about How to Map Parcels of the
> Cortex on the surface of the Brain Cortex
> To: "[email protected]" <[email protected]>
> Message-ID: <[email protected]>
> 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
>
>
>
>
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