Hi Freesurfer experts, I wanted to create a Freesurfer surface on some of the aseg ROIs. I was able to run mri_tesselate, mris_smooth, mris_inflate and mris_sphere some of the subcortical volumes for creating a surface.
The mri_sphere had a big chunk that was deleted and so I wanted to run mris_fix_topology to fix this issue. In trying to run this command it appears that mris_fix_topology tries to correct based off of a brain sphere (which this ROI is clearly not) and therefore it fails. I plan to then run subsequent steps such as mris_euler number and mris_remove_intersections
1) Is there any way to fix the topology of this ROI using freesurfer tools or a way to work around this issue? Do you feel the sphere is needed for a small subcortical surface (ie globus pallidus) or is this really more for complex structures such as cortical surfaces?
2) Is there a recommended set of steps to accomplish creating a surface from the ROI that is different from what I stated?
Thanks, Ajay
Hi Ajay
Florent Segonne developed some volumetric topology correction algorithms as well as surface-based ones when he was here. Try mri_topologycorrection and see how it works for you (although be warned that we haven't tried it in ages)
cheers Bruce
On Mon, 21 Mar 2016, Ajay Kurani wrote:
Hi Freesurfer experts, I wanted to create a Freesurfer surface on some of the aseg ROIs. I was able to run mri_tesselate, mris_smooth, mris_inflate and mris_sphere some of the subcortical volumes for creating a surface.
The mri_sphere had a big chunk that was deleted and so I wanted to run mris_fix_topology to fix this issue. In trying to run this command it appears that mris_fix_topology tries to correct based off of a brain sphere (which this ROI is clearly not) and therefore it fails. I plan to then run subsequent steps such as mris_euler number and mris_remove_intersections
- Is there any way to fix the topology of this ROI using freesurfer tools
or a way to work around this issue? Do you feel the sphere is needed for a small subcortical surface (ie globus pallidus) or is this really more for complex structures such as cortical surfaces?
- Is there a recommended set of steps to accomplish creating a surface from
the ROI that is different from what I stated?
Thanks, Ajay
Hello Freesurfer Experts,
I ran the following commands (from recon-all devtable) to create a surface model of the ROI's that I am interested in (they start off as a binary 1 mask):
1) mri_tesselate ../mri/lh.ROI.mgz 1 ../surf/lh.orig.nofix 2) mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 3) mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smooth.nofix 4) mris_inflate 5) mris_sphere 6) mri_fixtopology
When I use freeview the lh.smooth.nofix looks great. I wanted to use this file to create a surface and volume file, however mri_info lh.smooth.nofix comes up with the error of unknown filetype.
What is the lh.smooth.nofix filetype?
How would i be able to convert this lh.smooth.nofix to be used as a surface for surface-based analysis? Are there other files that need to be created first in order to convert this file to a surface? Is this file a label, annotation surface etc?
Thanks, Ajay
On Mon, Mar 21, 2016 at 1:03 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Freesurfer experts, I wanted to create a Freesurfer surface on some of the aseg ROIs. I was able to run mri_tesselate, mris_smooth, mris_inflate and mris_sphere some of the subcortical volumes for creating a surface.
The mri_sphere had a big chunk that was deleted and so I wanted to run mris_fix_topology to fix this issue. In trying to run this command it appears that mris_fix_topology tries to correct based off of a brain sphere (which this ROI is clearly not) and therefore it fails. I plan to then run subsequent steps such as mris_euler number and mris_remove_intersections
- Is there any way to fix the topology of this ROI using freesurfer tools
or a way to work around this issue? Do you feel the sphere is needed for a small subcortical surface (ie globus pallidus) or is this really more for complex structures such as cortical surfaces?
- Is there a recommended set of steps to accomplish creating a surface
from the ROI that is different from what I stated?
Thanks, Ajay
Hi Ajay
it's a surface file in our own (goofy) internal format. You can use mris_info to dump the header, or read it into matlab if you like
cheers Bruce
On Wed, 6 Apr 2016, Ajay Kurani wrote:
Hello Freesurfer Experts, I ran the following commands (from recon-all devtable) to create a surface model of the ROI's that I am interested in (they start off as a binary 1 mask):
- mri_tesselate ../mri/lh.ROI.mgz 1 ../surf/lh.orig.nofix
- mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smooth.nofix
- mris_inflate
- mris_sphere
- mri_fixtopology
When I use freeview the lh.smooth.nofix looks great. I wanted to use this file to create a surface and volume file, however mri_info lh.smooth.nofix comes up with the error of unknown filetype.
What is the lh.smooth.nofix filetype?
How would i be able to convert this lh.smooth.nofix to be used as a surface for surface-based analysis? Are there other files that need to be created first in order to convert this file to a surface? Is this file a label, annotation surface etc?
Thanks, Ajay
On Mon, Mar 21, 2016 at 1:03 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote: Hi Freesurfer experts, I wanted to create a Freesurfer surface on some of the aseg ROIs. I was able to run mri_tesselate, mris_smooth, mris_inflate and mris_sphere some of the subcortical volumes for creating a surface.
The mri_sphere had a big chunk that was deleted and so I wanted to run mris_fix_topology to fix this issue. In trying to run this command it appears that mris_fix_topology tries to correct based off of a brain sphere (which this ROI is clearly not) and therefore it fails. I plan to then run subsequent steps such as mris_euler number and mris_remove_intersections
- Is there any way to fix the topology of this ROI using freesurfer
tools or a way to work around this issue? Do you feel the sphere is needed for a small subcortical surface (ie globus pallidus) or is this really more for complex structures such as cortical surfaces?
- Is there a recommended set of steps to accomplish creating a
surface from the ROI that is different from what I stated?
Thanks, Ajay
Thanks for clarifying Bruce.
Just curious is there any freesurfer commands to convert this internal surface file into a .mgh file for external use? For example mri_surf2vol or mri_surf2label etc?
Thanks, Ajay
On Wed, Apr 6, 2016 at 5:17 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hello Freesurfer Experts,
I ran the following commands (from recon-all devtable) to create a surface model of the ROI's that I am interested in (they start off as a binary 1 mask):
- mri_tesselate ../mri/lh.ROI.mgz 1 ../surf/lh.orig.nofix
- mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smooth.nofix
- mris_inflate
- mris_sphere
- mri_fixtopology
When I use freeview the lh.smooth.nofix looks great. I wanted to use this file to create a surface and volume file, however mri_info lh.smooth.nofix comes up with the error of unknown filetype.
What is the lh.smooth.nofix filetype?
How would i be able to convert this lh.smooth.nofix to be used as a surface for surface-based analysis? Are there other files that need to be created first in order to convert this file to a surface? Is this file a label, annotation surface etc?
Thanks, Ajay
On Mon, Mar 21, 2016 at 1:03 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Freesurfer experts, I wanted to create a Freesurfer surface on some of the aseg ROIs. I was able to run mri_tesselate, mris_smooth, mris_inflate and mris_sphere some of the subcortical volumes for creating a surface.
The mri_sphere had a big chunk that was deleted and so I wanted to run mris_fix_topology to fix this issue. In trying to run this command it appears that mris_fix_topology tries to correct based off of a brain sphere (which this ROI is clearly not) and therefore it fails. I plan to then run subsequent steps such as mris_euler number and mris_remove_intersections
- Is there any way to fix the topology of this ROI using freesurfer
tools or a way to work around this issue? Do you feel the sphere is needed for a small subcortical surface (ie globus pallidus) or is this really more for complex structures such as cortical surfaces?
- Is there a recommended set of steps to accomplish creating a surface
from the ROI that is different from what I stated?
Thanks, Ajay
Hi Ajay
.mgh file doesn't store the necessary topological informations (neighbors, faces, and such) to store a surface. You can convert to gifti and some other modeling formats (or ascii)
cheers Bruce
On Wed, 6 Apr 2016, Ajay Kurani wrote:
Thanks for clarifying Bruce.
Just curious is there any freesurfer commands to convert this internal surface file into a .mgh file for external use? For example mri_surf2vol or mri_surf2label etc?
Thanks, Ajay
On Wed, Apr 6, 2016 at 5:17 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote: Hello Freesurfer Experts, I ran the following commands (from recon-all devtable) to create a surface model of the ROI's that I am interested in (they start off as a binary 1 mask):
- mri_tesselate ../mri/lh.ROI.mgz 1 ../surf/lh.orig.nofix
- mris_extract_main_component ../surf/lh.orig.nofix
../surf/lh.orig.nofix 3) mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smooth.nofix 4) mris_inflate 5) mris_sphere 6) mri_fixtopology
When I use freeview the lh.smooth.nofix looks great. I wanted to use this file to create a surface and volume file, however mri_info lh.smooth.nofix comes up with the error of unknown filetype.
What is the lh.smooth.nofix filetype?
How would i be able to convert this lh.smooth.nofix to be used as a surface for surface-based analysis? Are there other files that need to be created first in order to convert this file to a surface? Is this file a label, annotation surface etc?
Thanks, Ajay
On Mon, Mar 21, 2016 at 1:03 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote: Hi Freesurfer experts, I wanted to create a Freesurfer surface on some of the aseg ROIs. I was able to run mri_tesselate, mris_smooth, mris_inflate and mris_sphere some of the subcortical volumes for creating a surface.
The mri_sphere had a big chunk that was deleted and so I wanted to run mris_fix_topology to fix this issue. In trying to run this command it appears that mris_fix_topology tries to correct based off of a brain sphere (which this ROI is clearly not) and therefore it fails. I plan to then run subsequent steps such as mris_euler number and mris_remove_intersections
- Is there any way to fix the topology of this ROI using
freesurfer tools or a way to work around this issue? Do you feel the sphere is needed for a small subcortical surface (ie globus pallidus) or is this really more for complex structures such as cortical surfaces?
- Is there a recommended set of steps to accomplish creating a
surface from the ROI that is different from what I stated?
Thanks, Ajay
freesurfer@nmr.mgh.harvard.edu
-
Ajay Kurani -
Bruce Fischl