Re: [Freesurfer] Cortical surface analysis
See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 4/28/2021 5:18 PM, Fischl, Bruce wrote:
Yes, there is some documentation of how to do this on our website. I
defer to Doug on the particulars
Bruce
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *Ornaith O Reilly
*Sent:* Wednesday, April 28, 2021 4:30 PM
*To:* Freesurfer support list
*Subject:* Re: [Freesurfer] Cortical surface analysis
*External Email - Use Caution *
Hi Bruce,
Thanks a lot for this. What is the difference between RAS and surface
RAS?
Do I need to convert the surface RAS into RAS to be dealing in the
volume space?
Kind Regards,
Ornaith
On Tue, 27 Apr 2021 at 15:44, Fischl, Bruce <mailto:bfis...@mgh.harvard.edu>> wrote:
All the surface vertices are just listed in order. The patch keep
track of which vertex it corresponds to (so you can just use
pial_surface[patch.vno] or something).
The coordinates are documented on our website and are “surface ras”.
Cheers
Bruce
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> *On Behalf Of
*Ornaith O Reilly
*Sent:* Tuesday, April 27, 2021 8:02 AM
*To:* Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:* Re: [Freesurfer] Cortical surface analysis
*External Email - Use Caution *
Hi Bruce,
Yes I read in the patch the way that you're suggesting and I can
access the vino for the flat map. But how do i know the vertex
number of each vertex in the pial surface? Are they in order ?
Also, what coordinate system is the pial surface in when its read
into FreeSurfer? Is it RAS or surface RAS?
Kind Regards,
Ornaith
On Wed, 7 Apr 2021 at 20:02, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
How do you read it in? If you are using the read_patch.m that
we distribute it should be stored in patch.vno if you do:
>> patch = read_patch(path_file_name)
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> *On Behalf Of
*Ornaith O Reilly
*Sent:* Wednesday, April 7, 2021 2:29 PM
*To:* Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:* Re: [Freesurfer] Cortical surface analysis
*External Email - Use Caution *
Hi Bruce,
Thanks so much for your quick reply, I really appreciate your
help on this.
I don't understand how to recover the vertex index.
In Freeview I can see the vertex index number. When I load in
the data to MATLAB as discussed - the only thing that I have
access to are the coordinates of the vertices - not the vertex
index. How can I recover the vertex indices as well?
Thanks again.
Kind Regards,
Ornaith
On Tue, 6 Apr 2021 at 19:31, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Ornaith
The mapping uses the vertex index. That is, the vertex
index is stored in the flatmap, so you should always be
able to recover it, then look up the location of that
vertex on any other surface (of the same hemisphere/subject)
Cheers
Bruce
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> *On
Behalf Of *Ornaith O Reilly
*Sent:* Tuesday, April 6, 2021 2:19 PM
*To:* Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:* Re: [Freesurfer] Cortical surface analysis
*External Email - Use Caution *
Hello FreeSurfer developers,
Thanks a lot for your help. I have initialised the
pialxyz the way you suggested and made the flatmap in
MatLab using the read_patch function (screenshots
attached). I still don't understand how to convert
between the two. For example how to see what point
(x,y,z) on the pial surface corresponds to what (x,y)
point on the flatmap.
Thanks a lot for your help.
Kind Regards,
Ornaith
On Tue, 16 Mar 2021 at 15:58, Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>>
wrote:
On 3/8/2021 11:38 AM, Ornaith O Reilly wrote:
*External Email - Use Caution *
Hello Freesurfer developers,
I am
Re: [Freesurfer] Cortical surface analysis
Yes, there is some documentation of how to do this on our website. I defer to
Doug on the particulars
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Ornaith O Reilly
Sent: Wednesday, April 28, 2021 4:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical surface analysis
External Email - Use Caution
Hi Bruce,
Thanks a lot for this. What is the difference between RAS and surface RAS?
Do I need to convert the surface RAS into RAS to be dealing in the volume space?
Kind Regards,
Ornaith
On Tue, 27 Apr 2021 at 15:44, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
All the surface vertices are just listed in order. The patch keep track of
which vertex it corresponds to (so you can just use pial_surface[patch.vno] or
something).
The coordinates are documented on our website and are “surface ras”.
Cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Ornaith O Reilly
Sent: Tuesday, April 27, 2021 8:02 AM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Cortical surface analysis
External Email - Use Caution
Hi Bruce,
Yes I read in the patch the way that you're suggesting and I can access the
vino for the flat map. But how do i know the vertex number of each vertex in
the pial surface? Are they in order ?
Also, what coordinate system is the pial surface in when its read into
FreeSurfer? Is it RAS or surface RAS?
Kind Regards,
Ornaith
On Wed, 7 Apr 2021 at 20:02, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
How do you read it in? If you are using the read_patch.m that we distribute it
should be stored in patch.vno if you do:
>> patch = read_patch(path_file_name)
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Ornaith O Reilly
Sent: Wednesday, April 7, 2021 2:29 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Cortical surface analysis
External Email - Use Caution
Hi Bruce,
Thanks so much for your quick reply, I really appreciate your help on this.
I don't understand how to recover the vertex index.
In Freeview I can see the vertex index number. When I load in the data to
MATLAB as discussed - the only thing that I have access to are the coordinates
of the vertices - not the vertex index. How can I recover the vertex indices
as well?
Thanks again.
Kind Regards,
Ornaith
On Tue, 6 Apr 2021 at 19:31, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Ornaith
The mapping uses the vertex index. That is, the vertex index is stored in the
flatmap, so you should always be able to recover it, then look up the location
of that vertex on any other surface (of the same hemisphere/subject)
Cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Ornaith O Reilly
Sent: Tuesday, April 6, 2021 2:19 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Cortical surface analysis
External Email - Use Caution
Hello FreeSurfer developers,
Thanks a lot for your help. I have initialised the pialxyz the way you
suggested and made the flatmap in MatLab using the read_patch function
(screenshots attached). I still don't understand how to convert between the
two. For example how to see what point (x,y,z) on the pial surface corresponds
to what (x,y) point on the flatmap.
Thanks a lot for your help.
Kind Regards,
Ornaith
On Tue, 16 Mar 2021 at 15:58, Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:
On 3/8/2021 11:38 AM, Ornaith O Reilly wrote:
External Email - Use Caution
Hello Freesurfer developers,
I am new to Freesurfer and I'm hoping that someone can help me.
My goal is to be able to visualise electrodes contacts that are on lying on the
cortical surface on a flat map and a spherical map.
I've run recon-all and created the flatmap.
I'm using Matlab to achieve this and I've loaded the information with the lines
lhsphere =
fs_read_surf('/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.sphere');
lhflatpatch=fs_read_patch('/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.full.flat.patch.3D');
1. I want to be able to access the coordinates and show the electrons on the
flat map/ sphere and I was wondering how to do this? I understand that the
vertex ID number is what relates the coordinates in the original image to these
surfaces. I am wondering how to access the vertex ID numbers ? At the moment
I think that I only have access to the vertex
Re: [Freesurfer] Cortical surface analysis
External Email - Use Caution Hi Bruce, Thanks a lot for this. What is the difference between RAS and surface RAS? Do I need to convert the surface RAS into RAS to be dealing in the volume space? Kind Regards, Ornaith On Tue, 27 Apr 2021 at 15:44, Fischl, Bruce wrote: > All the surface vertices are just listed in order. The patch keep track of > which vertex it corresponds to (so you can just use pial_surface[patch.vno] > or something). > > > > The coordinates are documented on our website and are “surface ras”. > > > > Cheers > > Bruce > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Ornaith O Reilly > *Sent:* Tuesday, April 27, 2021 8:02 AM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Cortical surface analysis > > > > *External Email - Use Caution* > > Hi Bruce, > > > > Yes I read in the patch the way that you're suggesting and I can access > the vino for the flat map. But how do i know the vertex number of each > vertex in the pial surface? Are they in order ? > > > > Also, what coordinate system is the pial surface in when its read into > FreeSurfer? Is it RAS or surface RAS? > > > > Kind Regards, > > Ornaith > > > > On Wed, 7 Apr 2021 at 20:02, Fischl, Bruce > wrote: > > How do you read it in? If you are using the read_patch.m that we > distribute it should be stored in patch.vno if you do: > > > > >> patch = read_patch(path_file_name) > > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Ornaith O Reilly > *Sent:* Wednesday, April 7, 2021 2:29 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Cortical surface analysis > > > > *External Email - Use Caution* > > Hi Bruce, > > > > Thanks so much for your quick reply, I really appreciate your help on > this. > > > > I don't understand how to recover the vertex index. > > > > In Freeview I can see the vertex index number. When I load in the data to > MATLAB as discussed - the only thing that I have access to are the > coordinates of the vertices - not the vertex index. How can I recover the > vertex indices as well? > > > > Thanks again. > > > > Kind Regards, > > Ornaith > > > > > > On Tue, 6 Apr 2021 at 19:31, Fischl, Bruce > wrote: > > Hi Ornaith > > > > The mapping uses the vertex index. That is, the vertex index is stored in > the flatmap, so you should always be able to recover it, then look up the > location of that vertex on any other surface (of the same > hemisphere/subject) > > > > Cheers > > Bruce > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Ornaith O Reilly > *Sent:* Tuesday, April 6, 2021 2:19 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Cortical surface analysis > > > > *External Email - Use Caution* > > Hello FreeSurfer developers, > > > > Thanks a lot for your help. I have initialised the pialxyz the way you > suggested and made the flatmap in MatLab using the read_patch function > (screenshots attached). I still don't understand how to convert between > the two. For example how to see what point (x,y,z) on the pial surface > corresponds to what (x,y) point on the flatmap. > > > > Thanks a lot for your help. > > > > Kind Regards, > > Ornaith > > > > > > > > On Tue, 16 Mar 2021 at 15:58, Douglas N. Greve > wrote: > > > > On 3/8/2021 11:38 AM, Ornaith O Reilly wrote: > > *External Email - Use Caution* > > Hello Freesurfer developers, > > > > I am new to Freesurfer and I'm hoping that someone can help me. > > > > My goal is to be able to visualise electrodes contacts that are on lying > on the cortical surface on a flat map and a spherical map. > > > > I've run recon-all and created the flatmap. > > > > I'm using Matlab to achieve this and I've loaded the information with the > lines > > lhsphere = fs_read_surf( > '/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.sphere'); > > lhflatpatch=fs_read_patch( > '/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.full.flat.patch.3D' > ); > > > > 1. I want to be able to access the coordinates and show the electrons on > the flat map/ sphere and I was wondering how to do this?
Re: [Freesurfer] Cortical surface analysis
All the surface vertices are just listed in order. The patch keep track of
which vertex it corresponds to (so you can just use pial_surface[patch.vno] or
something).
The coordinates are documented on our website and are “surface ras”.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Ornaith O Reilly
Sent: Tuesday, April 27, 2021 8:02 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical surface analysis
External Email - Use Caution
Hi Bruce,
Yes I read in the patch the way that you're suggesting and I can access the
vino for the flat map. But how do i know the vertex number of each vertex in
the pial surface? Are they in order ?
Also, what coordinate system is the pial surface in when its read into
FreeSurfer? Is it RAS or surface RAS?
Kind Regards,
Ornaith
On Wed, 7 Apr 2021 at 20:02, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
How do you read it in? If you are using the read_patch.m that we distribute it
should be stored in patch.vno if you do:
>> patch = read_patch(path_file_name)
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Ornaith O Reilly
Sent: Wednesday, April 7, 2021 2:29 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Cortical surface analysis
External Email - Use Caution
Hi Bruce,
Thanks so much for your quick reply, I really appreciate your help on this.
I don't understand how to recover the vertex index.
In Freeview I can see the vertex index number. When I load in the data to
MATLAB as discussed - the only thing that I have access to are the coordinates
of the vertices - not the vertex index. How can I recover the vertex indices
as well?
Thanks again.
Kind Regards,
Ornaith
On Tue, 6 Apr 2021 at 19:31, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Ornaith
The mapping uses the vertex index. That is, the vertex index is stored in the
flatmap, so you should always be able to recover it, then look up the location
of that vertex on any other surface (of the same hemisphere/subject)
Cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Ornaith O Reilly
Sent: Tuesday, April 6, 2021 2:19 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Cortical surface analysis
External Email - Use Caution
Hello FreeSurfer developers,
Thanks a lot for your help. I have initialised the pialxyz the way you
suggested and made the flatmap in MatLab using the read_patch function
(screenshots attached). I still don't understand how to convert between the
two. For example how to see what point (x,y,z) on the pial surface corresponds
to what (x,y) point on the flatmap.
Thanks a lot for your help.
Kind Regards,
Ornaith
On Tue, 16 Mar 2021 at 15:58, Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:
On 3/8/2021 11:38 AM, Ornaith O Reilly wrote:
External Email - Use Caution
Hello Freesurfer developers,
I am new to Freesurfer and I'm hoping that someone can help me.
My goal is to be able to visualise electrodes contacts that are on lying on the
cortical surface on a flat map and a spherical map.
I've run recon-all and created the flatmap.
I'm using Matlab to achieve this and I've loaded the information with the lines
lhsphere =
fs_read_surf('/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.sphere');
lhflatpatch=fs_read_patch('/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.full.flat.patch.3D');
1. I want to be able to access the coordinates and show the electrons on the
flat map/ sphere and I was wondering how to do this? I understand that the
vertex ID number is what relates the coordinates in the original image to these
surfaces. I am wondering how to access the vertex ID numbers ? At the moment
I think that I only have access to the vertex coordinates and the vertex faces.
The easiest way to do this is probably to map the white or pial xyz into an mgz
file using mri_surf2surf, eg
mri_surf2surf --hemi lh --sval-xyz white --tval lh.white.xyz.mgz --s
yoursubject
You can then get the xyz of a given vertex by reading
whitexyz = MRIread('lh.white.xyz.mgz');
2. Additionally, I was wondering if there is a way to display the surface
images through Matlab? What would be the best way to show the surface with the
electrons overlaid on it?
I know there are ways, but I don't know their details
The version of Freesurfer and the platform that I'm using is outlined below:
1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551
2) Platform: macOS High Sierra 10.13.6
Re: [Freesurfer] Cortical surface analysis
External Email - Use Caution
Hi Bruce,
Yes I read in the patch the way that you're suggesting and I can access the
vino for the flat map. But how do i know the vertex number of each vertex
in the pial surface? Are they in order ?
Also, what coordinate system is the pial surface in when its read into
FreeSurfer? Is it RAS or surface RAS?
Kind Regards,
Ornaith
On Wed, 7 Apr 2021 at 20:02, Fischl, Bruce wrote:
> How do you read it in? If you are using the read_patch.m that we
> distribute it should be stored in patch.vno if you do:
>
>
>
> >> patch = read_patch(path_file_name)
>
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Ornaith O Reilly
> *Sent:* Wednesday, April 7, 2021 2:29 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Cortical surface analysis
>
>
>
> *External Email - Use Caution*
>
> Hi Bruce,
>
>
>
> Thanks so much for your quick reply, I really appreciate your help on
> this.
>
>
>
> I don't understand how to recover the vertex index.
>
>
>
> In Freeview I can see the vertex index number. When I load in the data to
> MATLAB as discussed - the only thing that I have access to are the
> coordinates of the vertices - not the vertex index. How can I recover the
> vertex indices as well?
>
>
>
> Thanks again.
>
>
>
> Kind Regards,
>
> Ornaith
>
>
>
>
>
> On Tue, 6 Apr 2021 at 19:31, Fischl, Bruce
> wrote:
>
> Hi Ornaith
>
>
>
> The mapping uses the vertex index. That is, the vertex index is stored in
> the flatmap, so you should always be able to recover it, then look up the
> location of that vertex on any other surface (of the same
> hemisphere/subject)
>
>
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Ornaith O Reilly
> *Sent:* Tuesday, April 6, 2021 2:19 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Cortical surface analysis
>
>
>
> *External Email - Use Caution*
>
> Hello FreeSurfer developers,
>
>
>
> Thanks a lot for your help. I have initialised the pialxyz the way you
> suggested and made the flatmap in MatLab using the read_patch function
> (screenshots attached). I still don't understand how to convert between
> the two. For example how to see what point (x,y,z) on the pial surface
> corresponds to what (x,y) point on the flatmap.
>
>
>
> Thanks a lot for your help.
>
>
>
> Kind Regards,
>
> Ornaith
>
>
>
>
>
>
>
> On Tue, 16 Mar 2021 at 15:58, Douglas N. Greve
> wrote:
>
>
>
> On 3/8/2021 11:38 AM, Ornaith O Reilly wrote:
>
> *External Email - Use Caution*
>
> Hello Freesurfer developers,
>
>
>
> I am new to Freesurfer and I'm hoping that someone can help me.
>
>
>
> My goal is to be able to visualise electrodes contacts that are on lying
> on the cortical surface on a flat map and a spherical map.
>
>
>
> I've run recon-all and created the flatmap.
>
>
>
> I'm using Matlab to achieve this and I've loaded the information with the
> lines
>
> lhsphere = fs_read_surf(
> '/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.sphere');
>
> lhflatpatch=fs_read_patch(
> '/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.full.flat.patch.3D'
> );
>
>
>
> 1. I want to be able to access the coordinates and show the electrons on
> the flat map/ sphere and I was wondering how to do this? I understand that
> the vertex ID number is what relates the coordinates in the original image
> to these surfaces. I am wondering how to access the vertex ID numbers ?
> At the moment I think that I only have access to the vertex coordinates and
> the vertex faces.
>
> The easiest way to do this is probably to map the white or pial xyz into
> an mgz file using mri_surf2surf, eg
> mri_surf2surf --hemi lh --sval-xyz white --tval lh.white.xyz.mgz --s
> yoursubject
> You can then get the xyz of a given vertex by reading
> whitexyz = MRIread('lh.white.xyz.mgz');
>
>
>
> 2. Additionally, I was wondering if there is a way to display the surface
> images through Matlab? What would be the best way to show the surface with
> the electrons overlaid on it?
>
> I know there are ways, but I don't know their details
>
>
>
> The version of Freesurfer and the platform that I'm using i
Re: [Freesurfer] Cortical surface analysis
How do you read it in? If you are using the read_patch.m that we distribute it
should be stored in patch.vno if you do:
>> patch = read_patch(path_file_name)
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Ornaith O Reilly
Sent: Wednesday, April 7, 2021 2:29 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical surface analysis
External Email - Use Caution
Hi Bruce,
Thanks so much for your quick reply, I really appreciate your help on this.
I don't understand how to recover the vertex index.
In Freeview I can see the vertex index number. When I load in the data to
MATLAB as discussed - the only thing that I have access to are the coordinates
of the vertices - not the vertex index. How can I recover the vertex indices
as well?
Thanks again.
Kind Regards,
Ornaith
On Tue, 6 Apr 2021 at 19:31, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Ornaith
The mapping uses the vertex index. That is, the vertex index is stored in the
flatmap, so you should always be able to recover it, then look up the location
of that vertex on any other surface (of the same hemisphere/subject)
Cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Ornaith O Reilly
Sent: Tuesday, April 6, 2021 2:19 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Cortical surface analysis
External Email - Use Caution
Hello FreeSurfer developers,
Thanks a lot for your help. I have initialised the pialxyz the way you
suggested and made the flatmap in MatLab using the read_patch function
(screenshots attached). I still don't understand how to convert between the
two. For example how to see what point (x,y,z) on the pial surface corresponds
to what (x,y) point on the flatmap.
Thanks a lot for your help.
Kind Regards,
Ornaith
On Tue, 16 Mar 2021 at 15:58, Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:
On 3/8/2021 11:38 AM, Ornaith O Reilly wrote:
External Email - Use Caution
Hello Freesurfer developers,
I am new to Freesurfer and I'm hoping that someone can help me.
My goal is to be able to visualise electrodes contacts that are on lying on the
cortical surface on a flat map and a spherical map.
I've run recon-all and created the flatmap.
I'm using Matlab to achieve this and I've loaded the information with the lines
lhsphere =
fs_read_surf('/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.sphere');
lhflatpatch=fs_read_patch('/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.full.flat.patch.3D');
1. I want to be able to access the coordinates and show the electrons on the
flat map/ sphere and I was wondering how to do this? I understand that the
vertex ID number is what relates the coordinates in the original image to these
surfaces. I am wondering how to access the vertex ID numbers ? At the moment
I think that I only have access to the vertex coordinates and the vertex faces.
The easiest way to do this is probably to map the white or pial xyz into an mgz
file using mri_surf2surf, eg
mri_surf2surf --hemi lh --sval-xyz white --tval lh.white.xyz.mgz --s
yoursubject
You can then get the xyz of a given vertex by reading
whitexyz = MRIread('lh.white.xyz.mgz');
2. Additionally, I was wondering if there is a way to display the surface
images through Matlab? What would be the best way to show the surface with the
electrons overlaid on it?
I know there are ways, but I don't know their details
The version of Freesurfer and the platform that I'm using is outlined below:
1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551
2) Platform: macOS High Sierra 10.13.6 (17G7024)
I really appreciate any help with this as I'm really stuck.
Thanks in advance for any help.
Kind Regards,
Ornaith O'Reilly
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Re: [Freesurfer] Cortical surface analysis
Hi Ornaith
The mapping uses the vertex index. That is, the vertex index is stored in the
flatmap, so you should always be able to recover it, then look up the location
of that vertex on any other surface (of the same hemisphere/subject)
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Ornaith O Reilly
Sent: Tuesday, April 6, 2021 2:19 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical surface analysis
External Email - Use Caution
Hello FreeSurfer developers,
Thanks a lot for your help. I have initialised the pialxyz the way you
suggested and made the flatmap in MatLab using the read_patch function
(screenshots attached). I still don't understand how to convert between the
two. For example how to see what point (x,y,z) on the pial surface corresponds
to what (x,y) point on the flatmap.
Thanks a lot for your help.
Kind Regards,
Ornaith
On Tue, 16 Mar 2021 at 15:58, Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:
On 3/8/2021 11:38 AM, Ornaith O Reilly wrote:
External Email - Use Caution
Hello Freesurfer developers,
I am new to Freesurfer and I'm hoping that someone can help me.
My goal is to be able to visualise electrodes contacts that are on lying on the
cortical surface on a flat map and a spherical map.
I've run recon-all and created the flatmap.
I'm using Matlab to achieve this and I've loaded the information with the lines
lhsphere =
fs_read_surf('/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.sphere');
lhflatpatch=fs_read_patch('/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.full.flat.patch.3D');
1. I want to be able to access the coordinates and show the electrons on the
flat map/ sphere and I was wondering how to do this? I understand that the
vertex ID number is what relates the coordinates in the original image to these
surfaces. I am wondering how to access the vertex ID numbers ? At the moment
I think that I only have access to the vertex coordinates and the vertex faces.
The easiest way to do this is probably to map the white or pial xyz into an mgz
file using mri_surf2surf, eg
mri_surf2surf --hemi lh --sval-xyz white --tval lh.white.xyz.mgz --s
yoursubject
You can then get the xyz of a given vertex by reading
whitexyz = MRIread('lh.white.xyz.mgz');
2. Additionally, I was wondering if there is a way to display the surface
images through Matlab? What would be the best way to show the surface with the
electrons overlaid on it?
I know there are ways, but I don't know their details
The version of Freesurfer and the platform that I'm using is outlined below:
1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551
2) Platform: macOS High Sierra 10.13.6 (17G7024)
I really appreciate any help with this as I'm really stuck.
Thanks in advance for any help.
Kind Regards,
Ornaith O'Reilly
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Re: [Freesurfer] Cortical surface analysis
External Email - Use Caution
Hello FreeSurfer developers,
Thanks a lot for your help. I have initialised the pialxyz the way you
suggested and made the flatmap in MatLab using the read_patch function
(screenshots attached). I still don't understand how to convert between
the two. For example how to see what point (x,y,z) on the pial surface
corresponds to what (x,y) point on the flatmap.
Thanks a lot for your help.
Kind Regards,
Ornaith
On Tue, 16 Mar 2021 at 15:58, Douglas N. Greve
wrote:
>
>
> On 3/8/2021 11:38 AM, Ornaith O Reilly wrote:
>
> External Email - Use Caution
> Hello Freesurfer developers,
>
> I am new to Freesurfer and I'm hoping that someone can help me.
>
> My goal is to be able to visualise electrodes contacts that are on lying
> on the cortical surface on a flat map and a spherical map.
>
> I've run recon-all and created the flatmap.
>
> I'm using Matlab to achieve this and I've loaded the information with the
> lines
>
> lhsphere = fs_read_surf(
> '/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.sphere');
> lhflatpatch=fs_read_patch(
> '/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.full.flat.patch.3D'
> );
>
> 1. I want to be able to access the coordinates and show the electrons on
> the flat map/ sphere and I was wondering how to do this? I understand that
> the vertex ID number is what relates the coordinates in the original image
> to these surfaces. I am wondering how to access the vertex ID numbers ?
> At the moment I think that I only have access to the vertex coordinates and
> the vertex faces.
>
> The easiest way to do this is probably to map the white or pial xyz into
> an mgz file using mri_surf2surf, eg
> mri_surf2surf --hemi lh --sval-xyz white --tval lh.white.xyz.mgz --s
> yoursubject
> You can then get the xyz of a given vertex by reading
> whitexyz = MRIread('lh.white.xyz.mgz');
>
>
> 2. Additionally, I was wondering if there is a way to display the surface
> images through Matlab? What would be the best way to show the surface with
> the electrons overlaid on it?
>
> I know there are ways, but I don't know their details
>
>
> The version of Freesurfer and the platform that I'm using is outlined
> below:
> 1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551
> 2) Platform: macOS High Sierra 10.13.6 (17G7024)
>
> I really appreciate any help with this as I'm really stuck.
>
> Thanks in advance for any help.
>
> Kind Regards,
> Ornaith O'Reilly
>
> ___
> Freesurfer mailing
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Cortical surface analysis
On 3/8/2021 11:38 AM, Ornaith O Reilly wrote:
External Email - Use Caution
Hello Freesurfer developers,
I am new to Freesurfer and I'm hoping that someone can help me.
My goal is to be able to visualise electrodes contacts that are on
lying on the cortical surface on a flat map and a spherical map.
I've run recon-all and created the flatmap.
I'm using Matlab to achieve this and I've loaded the information with
the lines
lhsphere =
fs_read_surf('/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.sphere');
lhflatpatch=fs_read_patch('/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.full.flat.patch.3D');
1. I want to be able to access the coordinates and show the electrons
on the flat map/ sphere and I was wondering how to do this? I
understand that the vertex ID number is what relates the coordinates
in the original image to these surfaces. I am wondering how to access
the vertex ID numbers ? At the moment I think that I only have access
to the vertex coordinates and the vertex faces.
The easiest way to do this is probably to map the white or pial xyz into
an mgz file using mri_surf2surf, eg
mri_surf2surf --hemi lh --sval-xyz white --tval lh.white.xyz.mgz
--s yoursubject
You can then get the xyz of a given vertex by reading
whitexyz = MRIread('lh.white.xyz.mgz');
2. Additionally, I was wondering if there is a way to display the
surface images through Matlab? What would be the best way to show the
surface with the electrons overlaid on it?
I know there are ways, but I don't know their details
The version of Freesurfer and the platform that I'm using is outlined
below:
1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551
2) Platform: macOS High Sierra 10.13.6 (17G7024)
I really appreciate any help with this as I'm really stuck.
Thanks in advance for any help.
Kind Regards,
Ornaith O'Reilly
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[Freesurfer] Cortical surface analysis
External Email - Use Caution Hello Freesurfer developers, I am new to Freesurfer and I'm hoping that someone can help me. My goal is to be able to visualise electrodes contacts that are on lying on the cortical surface on a flat map and a spherical map. I've run recon-all and created the flatmap. I'm using Matlab to achieve this and I've loaded the information with the lines lhsphere = fs_read_surf( '/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.sphere'); lhflatpatch=fs_read_patch( '/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.full.flat.patch.3D' ); 1. I want to be able to access the coordinates and show the electrons on the flat map/ sphere and I was wondering how to do this? I understand that the vertex ID number is what relates the coordinates in the original image to these surfaces. I am wondering how to access the vertex ID numbers ? At the moment I think that I only have access to the vertex coordinates and the vertex faces. 2. Additionally, I was wondering if there is a way to display the surface images through Matlab? What would be the best way to show the surface with the electrons overlaid on it? The version of Freesurfer and the platform that I'm using is outlined below: 1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 2) Platform: macOS High Sierra 10.13.6 (17G7024) I really appreciate any help with this as I'm really stuck. Thanks in advance for any help. Kind Regards, Ornaith O'Reilly ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
