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Dear Lilla,
Thanks for your help.
I have used the same command in the recon-all.log file (seen bellow), but I
have a doubt for the highlighted part in the command:
"mri_aparc2aseg --s SBJ1 --volmask --aseg aseg.presurf.hypos --relabel
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Dear Doug,
Special appreciation for your help. Actually, I have created the annotation
and the color table files and finally I have divided the parcels. Also, I
checked the primary and the division parcels on the .pial surface that they
were
and the
new output name.
On 8/1/2019 4:58 PM, Mahshid Fouladivanda wrote:
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Dear experts,
I have a segmentation file of all the tissues in the brain and the ribbon
file which were extracted by another toolbox rather than freesurfer. Also, I
have created the anno
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Dear Doug,
Thanks for your reply. I have used the same command in the recon-all.log
file (seen bellow), but I have a doubt for the highlighted part in the
command:
"mri_aparc2aseg --s SBJ1 --volmask --aseg aseg.presurf.hypos --relabel
mri/norm.mgz
External Email - Use Caution
Dear Lilla,
Thanks for your help.
I have used the same command in the recon-all.log file (seen bellow), but I
have a doubt for the highlighted part in the command:
"mri_aparc2aseg --s SBJ1 --volmask --aseg aseg.presurf.hypos --relabel
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Dear Experts,
I have a neonate MRI Image which its parcellation file, surface files and
the ribbon are not created by freesurfer. I have created an annotation file
for it using "write_annotation". Now, for further processing I need to use
External Email - Use Caution
Dear experts,
I have a segmentation file of all the tissues in the brain and the ribbon
file which were extracted by another toolbox rather than freesurfer. Also, I
have created the annotation file using "write_annotation.m". Now, I wanna
create a
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Dear Freesurfer Experts,
I would like to divide the surface parcellations of the neonatal brain. The
parcells were extracted using Draw_EM (Developing brain Region Annotation
With Expectation-Maximization), an atlas based segmentation, from
External Email - Use Caution
Dear experts,
I have a segmentation file of all the tissues in the brain and the ribbon
file which were extracted by another toolbox rather than freesurfer. Also, I
have created the annotation file using "write_annotation.m". Now, I wanna
create a
External Email - Use Caution
Dear Experts,
I have a neonate MRI Image which its parcellation file, surface files and
the ribbon are not created by freesurfer. I have created an annotation file
for it using "write_annotation". Now, for further processing I need to use
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Dear Bruce,
All the outputs are .nii and .gii
I do not know if it is possible to convert it to the annotation!
By the way, what is needed for creation of the annotation file? I mean what
information, it needs?
Regards
Mahshid
it is more specific
than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. Re: Skull Strip (Bruce Fischl)
2. How to Divide the Surface Parcellations of the Brain
(Mahshid Fouladivanda)
3. Re: How to Divide the Surface Parcellations of the Brain
(Bruce Fischl)
4.
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Dear Freesurfer Experts,
I would like to divide the surface parcellations of the neonatal brain. The
parcells were extracted using Draw_EM (Developing brain Region Annotation
With Expectation-Maximization), an atlas based segmentation, from
and
cerebellum and brainstem?? and then show them by using tksurfer or
tkmedit???
Regards,
Mahshid
From: Bruce Fischl
To: Mahshid Fouladivanda
Cc: freesurfer@nmr.mgh.harvard.edu, "dgr...@mgh.harvard.edu"
Date: Sun, 12 May 2019 10:47:23 -0400 (EDT)
Subject: Re: [Freesurfer] A Ques
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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
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Dear Freesurfer Experts,
I need a brain cortex surface including Brain-stem and Cerebellum. Using
"recon-all" command, Brain-stem and Cerebellum has been removed from the
output pial files. How can I set the command in order to keep up Brain-stem
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Dear Freesurfer Experts,
I have a predetermined cortical parcels in native space. I want to display
them on brain surface, As shown in the last image of page bellow:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview
I have
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Hi Dear experts,
I downloaded and installed freesurfer on CentOS without any problem and also
worked with it. Recently I've switched on mint 19 (an Debian based operating
system) and I tried to setup freesurfer but, it does not worked. I would
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