External Email - Use Caution
Dear Dr.Ficshl
Thanks a lot. So, As I understood, I should do the following steps:
1- Creating tessellations for cerebellum and brainstem so that the labels of them would be extracted
2- Adding the extracted labels to the surface file by using mri_vol2label, in order to create their surface as i make surface
3- Adding the extracted labels to the .annot file by using mris_sample_parc
Am I right???
And one more question, by creating the tessellations and extracting the labels, is it possible to create an surface including all cortical and cerebellum and brainstem?? and then show them by using tksurfer or tkmedit???
Regards, Mahshid 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 CautionHi,
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 CautionDear 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 CautionHello 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