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 new to Freesurf
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 coordinates and the vertex faces.
The easiest way to do
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? I understand that > the vertex ID number is what rel
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 (17G7024)
I really appreciate any help with this as I'm really stuck.
Tha
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 is outlined
> below:
>
> 1) FreeSurfer version: freesurfer-darwin-m
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
> https://secure-web.cisco.com/1Ogp5ZeoS72_H9fgRPteNOma_J9hPaTfdzd6HC3IGubCY3vT-6900ngXdEssiUKOEN83iJbaRuxNMiShdLlOKXEsjibjQ3746iu4iSesiMAO7FM0u9JNkAiZ3RbN0TT8aAzo0QUe3wE1wLOfCaW_LV58ZUFvu4Jp8VcRYtLlFq2jaZ4IhvfVwk9EAHZ2f2uNFvgXVQwrjI8lddgCE_MHRU2_3rGmlnYXAhqWlm22ouXXjaE7nx7oKhyinkx8WQ1Qz1t7wnWmQku8NFdH3eu0s6Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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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
Re: [Freesurfer] cortical surface area calculation
Yes, it will On 8/7/2020 6:27 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Hi all, Does this command calculate the Cortical Surface Area without the non-cortical Medial Wall?? mris_calc --label ../label/lh.cortex.label lh.area stats Jim The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] cortical surface area calculation
External Email - Use Caution Hi all, Does this command calculate the Cortical Surface Area without the non-cortical Medial Wall?? mris_calc --label ../label/lh.cortex.label lh.area stats Jim The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cortical surface
External Email - Use Caution OK. Thank you very much. Sincerely, Zheng At 2018-08-13 01:15:26, "Douglas Greve" wrote: You can break up the aparc annotation into labels (mri_annotation2label), then create a new annotation with just the insula (mris_label2annot) On 8/12/18 5:17 AM, 郑凤莲 wrote: External Email - Use Caution Dear experts, I an using FS 6.0 for cortical reconstructions. I can show whole brain regions (tksurfer...), as shown in the picture. However, I just want to show insular region. Is there any way to complete it? I am looking forward to your reply. Thanks very much. Sincerely, Zheng ___ Freesurfer mailing list freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Cortical surface
You can break up the aparc annotation into labels (mri_annotation2label), then create a new annotation with just the insula (mris_label2annot) On 8/12/18 5:17 AM, 郑凤莲 wrote: External Email - Use Caution Dear experts, I an using FS 6.0 for cortical reconstructions. I can show whole brain regions (tksurfer...), as shown in the picture. However, I just want to show insular region. Is there any way to complete it? I am looking forward to your reply. Thanks very much. Sincerely, Zheng ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Cortical surface
External Email - Use Caution Dear experts, I an using FS 6.0 for cortical reconstructions. I can show whole brain regions (tksurfer...), as shown in the picture. However, I just want to show insular region. Is there any way to complete it? I am looking forward to your reply. Thanks very much. Sincerely, Zheng___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] cortical surface area
Thank you for the input. Jim -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Friday, October 13, 2017 10:09 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cortical surface area The 2nd is the one you want as the first one includes non cortical structures in the medial wall. On 10/12/17 6:35 PM, Alexopoulos, Dimitrios wrote: > Thanks. > > I ran this command: > mris_anatomical_stats subjectID lh pial > It gave me a total surface area of 115007 mm^2 > > I also tried the following command from within the 'label' directory: > mris_anatomical_stats -l lh.cortex.label -f lh.cortex.stats -b subjectID lh > pial > It gave me a total surface area 109458 mm^2 > > Which is the correct method and value for total cortical surface area? > > Jim > > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Thursday, October 12, 2017 5:17 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] cortical surface area > > oh, sorry, I missed the 5.3 part. YOu can always compute it for a subject > via: > > mris_anatomical_stats pial > > cheers > Bruce > On Thu, 12 Oct 2017, > Alexopoulos, Dimitrios wrote: > >> I don't see this file in the stats directory using FS 5.3. >> >> Jim >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce >> Fischl >> Sent: Thursday, October 12, 2017 4:52 PM >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] cortical surface area >> >> Hi Jim >> >> check the ?h.aparc.pial.stats file. I think the total surface area should be >> in there. >> >> cheers >> Bruce >> On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote: >> >>> Specifically, where in the aparc.stats file (or other file) is the cortical >>> surface area? >>> I only see default output for 'WhiteSurfArea'. >>> >>> Jim >>> >>> >>> -Original Message- >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas >>> N Greve >>> Sent: Thursday, October 12, 2017 4:16 PM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] cortical surface area >>> >>> mm2 >>> >>> >>> On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote: >>>> What measure is for the cortical surface area? >>>> >>>> The measure in the aparc.stats file states 'WhiteSurfArea' >>>> >>>> Jim >>>> >>>> >>>> - >>>> - >>>> -- >>>> >>>> The materials in this message are private and may contain Protected >>>> Healthcare Information or other information of a sensitive nature. >>>> If you are not the intended recipient, be advised that any >>>> unauthorized use, disclosure, copying or the taking of any action in >>>> reliance on the contents of this information is strictly prohibited. >>>> If you have received this email in error, please immediately notify >>>> the sender via telephone or return mail. >>>> >>>> >>>> >>>> ___ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom
Re: [Freesurfer] cortical surface area
that is the area of the white matter surface in mm2 On 10/12/17 2:15 PM, Alexopoulos, Dimitrios wrote: What measure is for the cortical surface area? The measure in the aparc.stats file states ‘WhiteSurfArea’ Jim The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] cortical surface area
The 2nd is the one you want as the first one includes non cortical structures in the medial wall. On 10/12/17 6:35 PM, Alexopoulos, Dimitrios wrote: > Thanks. > > I ran this command: > mris_anatomical_stats subjectID lh pial > It gave me a total surface area of 115007 mm^2 > > I also tried the following command from within the 'label' directory: > mris_anatomical_stats -l lh.cortex.label -f lh.cortex.stats -b subjectID lh > pial > It gave me a total surface area 109458 mm^2 > > Which is the correct method and value for total cortical surface area? > > Jim > > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Thursday, October 12, 2017 5:17 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] cortical surface area > > oh, sorry, I missed the 5.3 part. YOu can always compute it for a subject > via: > > mris_anatomical_stats pial > > cheers > Bruce > On Thu, 12 Oct 2017, > Alexopoulos, Dimitrios wrote: > >> I don't see this file in the stats directory using FS 5.3. >> >> Jim >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce >> Fischl >> Sent: Thursday, October 12, 2017 4:52 PM >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] cortical surface area >> >> Hi Jim >> >> check the ?h.aparc.pial.stats file. I think the total surface area should be >> in there. >> >> cheers >> Bruce >> On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote: >> >>> Specifically, where in the aparc.stats file (or other file) is the cortical >>> surface area? >>> I only see default output for 'WhiteSurfArea'. >>> >>> Jim >>> >>> >>> -Original Message- >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas >>> N Greve >>> Sent: Thursday, October 12, 2017 4:16 PM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] cortical surface area >>> >>> mm2 >>> >>> >>> On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote: >>>> What measure is for the cortical surface area? >>>> >>>> The measure in the aparc.stats file states 'WhiteSurfArea' >>>> >>>> Jim >>>> >>>> >>>> - >>>> - >>>> -- >>>> >>>> The materials in this message are private and may contain Protected >>>> Healthcare Information or other information of a sensitive nature. >>>> If you are not the intended recipient, be advised that any >>>> unauthorized use, disclosure, copying or the taking of any action in >>>> reliance on the contents of this information is strictly prohibited. >>>> If you have received this email in error, please immediately notify >>>> the sender via telephone or return mail. >>>> >>>> >>>> >>>> ___ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom it >>> is addressed. If you believe this e-mail was sent to you in error and the >>> e-mail contains patient information, please contact the Partners Compliance >>> HelpLine at http://www.partners.org/complianceline . If the e-mail was sent >>> to you in error but does not con
Re: [Freesurfer] cortical surface area
Thanks. I ran this command: mris_anatomical_stats subjectID lh pial It gave me a total surface area of 115007 mm^2 I also tried the following command from within the 'label' directory: mris_anatomical_stats -l lh.cortex.label -f lh.cortex.stats -b subjectID lh pial It gave me a total surface area 109458 mm^2 Which is the correct method and value for total cortical surface area? Jim -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, October 12, 2017 5:17 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] cortical surface area oh, sorry, I missed the 5.3 part. YOu can always compute it for a subject via: mris_anatomical_stats pial cheers Bruce On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote: > I don't see this file in the stats directory using FS 5.3. > > Jim > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce > Fischl > Sent: Thursday, October 12, 2017 4:52 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] cortical surface area > > Hi Jim > > check the ?h.aparc.pial.stats file. I think the total surface area should be > in there. > > cheers > Bruce > On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote: > >> Specifically, where in the aparc.stats file (or other file) is the cortical >> surface area? >> I only see default output for 'WhiteSurfArea'. >> >> Jim >> >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas >> N Greve >> Sent: Thursday, October 12, 2017 4:16 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] cortical surface area >> >> mm2 >> >> >> On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote: >>> >>> What measure is for the cortical surface area? >>> >>> The measure in the aparc.stats file states 'WhiteSurfArea' >>> >>> Jim >>> >>> >>> - >>> - >>> -- >>> >>> The materials in this message are private and may contain Protected >>> Healthcare Information or other information of a sensitive nature. >>> If you are not the intended recipient, be advised that any >>> unauthorized use, disclosure, copying or the taking of any action in >>> reliance on the contents of this information is strictly prohibited. >>> If you have received this email in error, please immediately notify >>> the sender via telephone or return mail. >>> >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail contains patient information, please contact the Partners Compliance >> HelpLine at http://www.partners.org/complianceline . If the e-mail was sent >> to you in error but does not contain patient information, please contact the >> sender and properly dispose of the e-mail. >> >> >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying or the taking of any action in reliance on the contents >> of this information is strictly prohibited. If you have received this email >> in error, please immediately notify the sender via telephone or return
Re: [Freesurfer] cortical surface area
oh, sorry, I missed the 5.3 part. YOu can always compute it for a subject via: mris_anatomical_stats pial cheers Bruce On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote: > I don't see this file in the stats directory using FS 5.3. > > Jim > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Thursday, October 12, 2017 4:52 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] cortical surface area > > Hi Jim > > check the ?h.aparc.pial.stats file. I think the total surface area should be > in there. > > cheers > Bruce > On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote: > >> Specifically, where in the aparc.stats file (or other file) is the cortical >> surface area? >> I only see default output for 'WhiteSurfArea'. >> >> Jim >> >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N >> Greve >> Sent: Thursday, October 12, 2017 4:16 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] cortical surface area >> >> mm2 >> >> >> On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote: >>> >>> What measure is for the cortical surface area? >>> >>> The measure in the aparc.stats file states 'WhiteSurfArea' >>> >>> Jim >>> >>> - >>> - >>> -- >>> >>> The materials in this message are private and may contain Protected >>> Healthcare Information or other information of a sensitive nature. If >>> you are not the intended recipient, be advised that any unauthorized >>> use, disclosure, copying or the taking of any action in reliance on >>> the contents of this information is strictly prohibited. If you have >>> received this email in error, please immediately notify the sender >>> via telephone or return mail. >>> >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail contains patient information, please contact the Partners Compliance >> HelpLine at http://www.partners.org/complianceline . If the e-mail was sent >> to you in error but does not contain patient information, please contact the >> sender and properly dispose of the e-mail. >> >> >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying or the taking of any action in reliance on the contents >> of this information is strictly prohibited. If you have received this email >> in error, please immediately notify the sender via telephone or return mail. >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return mail. > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cortical surface area
I don't see this file in the stats directory using FS 5.3. Jim -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, October 12, 2017 4:52 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] cortical surface area Hi Jim check the ?h.aparc.pial.stats file. I think the total surface area should be in there. cheers Bruce On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote: > Specifically, where in the aparc.stats file (or other file) is the cortical > surface area? > I only see default output for 'WhiteSurfArea'. > > Jim > > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N > Greve > Sent: Thursday, October 12, 2017 4:16 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] cortical surface area > > mm2 > > > On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote: >> >> What measure is for the cortical surface area? >> >> The measure in the aparc.stats file states 'WhiteSurfArea' >> >> Jim >> >> - >> - >> -- >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If >> you are not the intended recipient, be advised that any unauthorized >> use, disclosure, copying or the taking of any action in reliance on >> the contents of this information is strictly prohibited. If you have >> received this email in error, please immediately notify the sender >> via telephone or return mail. >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at http://www.partners.org/complianceline . If the e-mail was sent to you in > error but does not contain patient information, please contact the sender and > properly dispose of the e-mail. > > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return mail. > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cortical surface area
Hi Jim check the ?h.aparc.pial.stats file. I think the total surface area should be in there. cheers Bruce On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote: > Specifically, where in the aparc.stats file (or other file) is the cortical > surface area? > I only see default output for 'WhiteSurfArea'. > > Jim > > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Thursday, October 12, 2017 4:16 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] cortical surface area > > mm2 > > > On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote: >> >> What measure is for the cortical surface area? >> >> The measure in the aparc.stats file states 'WhiteSurfArea' >> >> Jim >> >> -- >> -- >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If >> you are not the intended recipient, be advised that any unauthorized >> use, disclosure, copying or the taking of any action in reliance on >> the contents of this information is strictly prohibited. If you have >> received this email in error, please immediately notify the sender via >> telephone or return mail. >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at http://www.partners.org/complianceline . If the e-mail was sent to you in > error but does not contain patient information, please contact the sender and > properly dispose of the e-mail. > > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return mail. > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cortical surface area
Specifically, where in the aparc.stats file (or other file) is the cortical surface area? I only see default output for 'WhiteSurfArea'. Jim -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, October 12, 2017 4:16 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cortical surface area mm2 On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote: > > What measure is for the cortical surface area? > > The measure in the aparc.stats file states 'WhiteSurfArea' > > Jim > > -- > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying or the taking of any action in reliance on > the contents of this information is strictly prohibited. If you have > received this email in error, please immediately notify the sender via > telephone or return mail. > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cortical surface area
mm2 On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote: > > What measure is for the cortical surface area? > > The measure in the aparc.stats file states ‘WhiteSurfArea’ > > Jim > > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying or the taking of any action in reliance on > the contents of this information is strictly prohibited. If you have > received this email in error, please immediately notify the sender via > telephone or return mail. > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] cortical surface area
What measure is for the cortical surface area? The measure in the aparc.stats file states 'WhiteSurfArea' Jim The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] cortical surface pattern matching
Hi Greg you could threshold then look at Hausdorff distance of the blobs. Or you could smooth before computing correlation as that will take spatial stuff into account. Or if you have a patch that you want to cross-correlate against the rest of the surface you could do it on the sphere, although that's a bit of a pain since you have to take the metric tensor into account cheers Bruce On Tue, 21 Jun 2016, GREGORY R KIRK wrote: > > Hi, > > > has anyone created functionality to compare the spatial > correlation/similarity > > of two patterns in the form of cortical surface overlays. What I am looking > at is a have > > scalar at every point on the cortical surface. obviously this is just a list > of vertices with > > a scalar value associated with each. obviously I can map these both onto an > average cortical surface and then simply compute the correlation of both of > these. > > > but of course pattern similarity is an inherently spatial problem and for > cortical > > surfaces a 2 dimensional spatial correlation or other similarity metric > would be > > what you want. Here the order of vertices in a vertex list maps somewhat > like a > > string around the cortex and so the next wrap around you have vertices which > are > > adjacent on the surface but distant by the metric of vertex count. > > > is there any implementation of a similarity metric which takes this > coordinate problem into account. In my measure every vertex across both hemi > has a value and so i am not interested in something for a small localized > patch. > > > any thoughts appreciated > > > Greg > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] cortical surface pattern matching
Hi, has anyone created functionality to compare the spatial correlation/similarity of two patterns in the form of cortical surface overlays. What I am looking at is a have scalar at every point on the cortical surface. obviously this is just a list of vertices with a scalar value associated with each. obviously I can map these both onto an average cortical surface and then simply compute the correlation of both of these. but of course pattern similarity is an inherently spatial problem and for cortical surfaces a 2 dimensional spatial correlation or other similarity metric would be what you want. Here the order of vertices in a vertex list maps somewhat like a string around the cortex and so the next wrap around you have vertices which are adjacent on the surface but distant by the metric of vertex count. is there any implementation of a similarity metric which takes this coordinate problem into account. In my measure every vertex across both hemi has a value and so i am not interested in something for a small localized patch. any thoughts appreciated Greg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] cortical surface area measurement and vertex-wise analysis
Hi Emma, Please, see below: On 13 October 2014 20:11, Emma Thompson vonecono...@gmail.com wrote: Hi Anderson, Thank you for your paper. I guess I am confused. I have analyzed my structural data with qdec, specifically looking at a measure of cortical thickness and volume. I'm considering looking at surface area as well but was told it wasn't a very good measure using qdec, I have no other information really. Could you speak to whether or not this measure is valid in so far as one runs it using qdec? The data that is used in qdec comes from mris_preproc, which uses vertexwise interpolation with Jacobian correction for local stretches/shrinkages. The amount of area is preserved globally, which is desirable, although locally it's something difficult to achieve. If without any smoothing, the spatial correlation between mris_preproc and the method in the paper is about 0.65, and the correlation at a given vertex, across subjects, varies spatially. Note, however, that the smoothing -- that is applied by default -- should increase the correlation vastly, but I don't have the exact numbers at hand to provide yet. For area, as well as for volume, the method shown in the paper is really the gold standard: it's pycnophylactic and thus guarantees that the amount of area is preserved locally everywhere in the brain during the interpolation. It's the same method used in GIS applications for geoprocessing. The downside is that the current implementation, using Matlab, is too slow (for the ico7, it can well take 10-15h per hemisphere in a single CPU). Also, in your opinion, would it be redundant to look at surface area in addition to measures of cortical thickness and cortical volume? Actually, the redundant bit here is volume. Area and thickness are uncorrelated phenotypically and genetically, and each provide different pieces of information (this is shown here http://dx.doi.org/10.1093/cercor/bhp026 and here http://www.sciencedirect.com/science/article/pii/S1053811909013160). Volume is a mixture of both, in proportions that vary across the cortical mantle. I would not consider using volume given that thickness and area are available. Moreover, volume is also an areal quantity in the sense that it requires the same methods for interpolation as surface area itself, so all that is said above about area applies also to cortical volumes. Hope this helps! All the best, Anderson On Sun, Oct 12, 2014 at 3:00 PM, Anderson M. Winkler wink...@fmrib.ox.ac.uk wrote: Hi Donna, In that same paper we also comment on the differences between expansion/contraction and absolute areal measurements assessed at each face of the surface (i.e., facewise), which can, after interpolation, be converted to vertexwise to facilitate analysis using current tools (e.g., mri_glmfit or qdec), without loss of areal quantities. All the best, Anderson On 11 October 2014 04:05, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Emma, I might not be the only one who is unsure what you mean by a vertex-wise cortical surface area measure. Do you mean something like what is illustrated in figures 2 and 3 here: http://www.pnas.org/content/107/29/13135.figures-only ... which is similar, but not identical to the local gyrification index? If so, would you use this measure on surfaces before or after registration to a target atlas? Donna On Oct 10, 2014, at 4:19 PM, Emma Thompson vonecono...@gmail.com wrote: Dear Freesurfers, I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] cortical surface area measurement and vertex-wise analysis
If you are using --qcache, then there is nothing wrong specifically with the qdec implementation On 10/13/2014 03:11 PM, Emma Thompson wrote: Hi Anderson, Thank you for your paper. I guess I am confused. I have analyzed my structural data with qdec, specifically looking at a measure of cortical thickness and volume. I'm considering looking at surface area as well but was told it wasn't a very good measure using qdec, I have no other information really. Could you speak to whether or not this measure is valid in so far as one runs it using qdec? Also, in your opinion, would it be redundant to look at surface area in addition to measures of cortical thickness and cortical volume? Thanks for your help and apologizes for my silly questions. On Sun, Oct 12, 2014 at 3:00 PM, Anderson M. Winkler wink...@fmrib.ox.ac.uk mailto:wink...@fmrib.ox.ac.uk wrote: Hi Donna, In that same paper we also comment on the differences between expansion/contraction and absolute areal measurements assessed at each face of the surface (i.e., facewise), which can, after interpolation, be converted to vertexwise to facilitate analysis using current tools (e.g., mri_glmfit or qdec), without loss of areal quantities. All the best, Anderson On 11 October 2014 04:05, Donna Dierker do...@brainvis.wustl.edu mailto:do...@brainvis.wustl.edu wrote: Hi Emma, I might not be the only one who is unsure what you mean by a vertex-wise cortical surface area measure. Do you mean something like what is illustrated in figures 2 and 3 here: http://www.pnas.org/content/107/29/13135.figures-only … which is similar, but not identical to the local gyrification index? If so, would you use this measure on surfaces before or after registration to a target atlas? Donna On Oct 10, 2014, at 4:19 PM, Emma Thompson vonecono...@gmail.com mailto:vonecono...@gmail.com wrote: Dear Freesurfers, I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cortical surface area measurement and vertex-wise analysis
Hi Anderson, Thank you for your paper. I guess I am confused. I have analyzed my structural data with qdec, specifically looking at a measure of cortical thickness and volume. I'm considering looking at surface area as well but was told it wasn't a very good measure using qdec, I have no other information really. Could you speak to whether or not this measure is valid in so far as one runs it using qdec? Also, in your opinion, would it be redundant to look at surface area in addition to measures of cortical thickness and cortical volume? Thanks for your help and apologizes for my silly questions. On Sun, Oct 12, 2014 at 3:00 PM, Anderson M. Winkler wink...@fmrib.ox.ac.uk wrote: Hi Donna, In that same paper we also comment on the differences between expansion/contraction and absolute areal measurements assessed at each face of the surface (i.e., facewise), which can, after interpolation, be converted to vertexwise to facilitate analysis using current tools (e.g., mri_glmfit or qdec), without loss of areal quantities. All the best, Anderson On 11 October 2014 04:05, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Emma, I might not be the only one who is unsure what you mean by a vertex-wise cortical surface area measure. Do you mean something like what is illustrated in figures 2 and 3 here: http://www.pnas.org/content/107/29/13135.figures-only … which is similar, but not identical to the local gyrification index? If so, would you use this measure on surfaces before or after registration to a target atlas? Donna On Oct 10, 2014, at 4:19 PM, Emma Thompson vonecono...@gmail.com wrote: Dear Freesurfers, I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] cortical surface area measurement and vertex-wise analysis
Hi Emma, Could you clarify what would be the disadvantages that you've heard about? I ask because we've studied and tried to clarify many aspects of the analysis of surface area in this paper http://www.sciencedirect.com/science/article/pii/S1053811912002996. Maybe if there's something not covered there we could try to comment then. Thanks! All the best, Anderson On 10 October 2014 22:19, Emma Thompson vonecono...@gmail.com wrote: Dear Freesurfers, I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] cortical surface area measurement and vertex-wise analysis
Hi Donna, In that same paper we also comment on the differences between expansion/contraction and absolute areal measurements assessed at each face of the surface (i.e., facewise), which can, after interpolation, be converted to vertexwise to facilitate analysis using current tools (e.g., mri_glmfit or qdec), without loss of areal quantities. All the best, Anderson On 11 October 2014 04:05, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Emma, I might not be the only one who is unsure what you mean by a vertex-wise cortical surface area measure. Do you mean something like what is illustrated in figures 2 and 3 here: http://www.pnas.org/content/107/29/13135.figures-only ... which is similar, but not identical to the local gyrification index? If so, would you use this measure on surfaces before or after registration to a target atlas? Donna On Oct 10, 2014, at 4:19 PM, Emma Thompson vonecono...@gmail.com wrote: Dear Freesurfers, I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] cortical surface area measurement and vertex-wise analysis
Dear Freesurfers, I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] cortical surface area measurement and vertex-wise analysis
Hi Emma, I might not be the only one who is unsure what you mean by a vertex-wise cortical surface area measure. Do you mean something like what is illustrated in figures 2 and 3 here: http://www.pnas.org/content/107/29/13135.figures-only … which is similar, but not identical to the local gyrification index? If so, would you use this measure on surfaces before or after registration to a target atlas? Donna On Oct 10, 2014, at 4:19 PM, Emma Thompson vonecono...@gmail.com wrote: Dear Freesurfers, I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Cortical surface
Dear Freesurfer experts, I am interested in running cortical surface area on longitudinal data from MRI scans and run multisubject comparisons (patients vs controls). I would like to ask you where could I find either a tutorial or a guide for performing such analysis. Also I am not familiar with freesurfer, so I am not sure which type of preprocessing should be undertaken.I would greatly appreciate your valuable help on this topic.Pablo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] cortical surface area related measures
Regarding Winkler et al.: http://brainder.org/2012/06/02/facewise-brain-cortical-surface-area-scripts-now-available/ On Aug 21, 2012 11:00 PM, Gregory Kirk gk...@wisc.edu wrote: Hi folks, I wanted to make sure i have everything straight w.r.t. the surface area measures. as i see there are 4 ways implemented ( somewhere ) to do cortical surface area analysis. 1. areal expansion 2. Local Gyrification Index 3. direct vertex based true surface area glm, Winkler AM et. al 4. roi based, i.e. based on the surface areas of the parcellation units in lh.aparc.a2009s.stats etc. 1. recent pub, Lisa T. Eyler et. al used the areal expansion method. was this done exactly as would be achived by using the area tab on qdec and setting up a glm ? Dale published surface area specifying some details of implementation but i was not sure if this was exactly what is implemented in qdec ? 2. LGI seems to me this is the ratio of two areas, that of the hull to the area inscribed by projecting the border of the hull onto the grey/white surface. In an e-mail Nick said LGI is a curvature based measure and that confused me a bit. gyrification is of course related to curvature but it seems the quantities actually calculated here are ratios of areas, which gives local info on surface area differences. 3. the winkler stuff is i think not publicly available yet at this time ? 4. straightforward enough not withstanding ICV corrections, etc. any words of clarification before i start trying some analysis on my group ? thank you Greg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] cortical surface area related measures
Hi folks, I wanted to make sure i have everything straight w.r.t. the surface area measures. as i see there are 4 ways implemented ( somewhere ) to do cortical surface area analysis. 1. areal expansion 2. Local Gyrification Index 3. direct vertex based true surface area glm, Winkler AM et. al 4. roi based, i.e. based on the surface areas of the parcellation units in lh.aparc.a2009s.stats etc. 1. recent pub, Lisa T. Eyler et. al used the areal expansion method. was this done exactly as would be achived by using the area tab on qdec and setting up a glm ? Dale published surface area specifying some details of implementation but i was not sure if this was exactly what is implemented in qdec ? 2. LGI seems to me this is the ratio of two areas, that of the hull to the area inscribed by projecting the border of the hull onto the grey/white surface. In an e-mail Nick said LGI is a curvature based measure and that confused me a bit. gyrification is of course related to curvature but it seems the quantities actually calculated here are ratios of areas, which gives local info on surface area differences. 3. the winkler stuff is i think not publicly available yet at this time ? 4. straightforward enough not withstanding ICV corrections, etc. any words of clarification before i start trying some analysis on my group ? thank you Greg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] cortical surface area related measures
Hi Greg, I don't know what areal expansion refers to. If you want to use area (eg, the area tab in qdec), you should make sure to download the most recent version of mris_preproc (which performs a jacobian type correction) ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc doug On 08/21/2012 04:59 PM, Gregory Kirk wrote: Hi folks, I wanted to make sure i have everything straight w.r.t. the surface area measures. as i see there are 4 ways implemented ( somewhere ) to do cortical surface area analysis. 1. areal expansion 2. Local Gyrification Index 3. direct vertex based true surface area glm, Winkler AM et. al 4. roi based, i.e. based on the surface areas of the parcellation units in lh.aparc.a2009s.stats etc. 1. recent pub, Lisa T. Eyler et. al used the areal expansion method. was this done exactly as would be achived by using the area tab on qdec and setting up a glm ? Dale published surface area specifying some details of implementation but i was not sure if this was exactly what is implemented in qdec ? 2. LGI seems to me this is the ratio of two areas, that of the hull to the area inscribed by projecting the border of the hull onto the grey/white surface. In an e-mail Nick said LGI is a curvature based measure and that confused me a bit. gyrification is of course related to curvature but it seems the quantities actually calculated here are ratios of areas, which gives local info on surface area differences. 3. the winkler stuff is i think not publicly available yet at this time ? 4. straightforward enough not withstanding ICV corrections, etc. any words of clarification before i start trying some analysis on my group ? thank you Greg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] cortical surface of individual subject: coordinates in individual's MNI space
For #1, it might be easier to use mri_surf2surf with the --sval-tal-xyz option. See the --help for more info. doug Bruce Fischl wrote: 1. Yes, just apply the talairach.xfm transform to each vertex. Should be easy enough to do in matlab using read_surf.m. 2. Yes, this can also be done in matlab, saving either in curv (write_curv.m) or wfile format. On Sat, 22 Oct 2011, Nela Cicmil wrote: Dear Freesurfer Developers and Users, I have two question(s) about Freesurfer and individual subject's MNI coordinates: (1) Having run recon-all to reconstruct the cortical surface for an individual subject in my study, is it possible to obtain the list of coordinates that describe the points in the individual subject's MNI space that comprise the cortical surface of that subject's brain? This is in order to run an MEG beamformer analysis (in matlab) in the subject's own MNI space, but restricted to those voxels that comprise the cortical surface for that subject, as calculated by Freesurfer. (2) Once I have obtained (in matlab), for a list of voxels that comprise the cortical surface, each of the their MNI coordinates and their associated activation value (e.g. tstat), is there a straightforward way to display this on the cortical surface of that subject in tksurfer, for example by converting to a simple wfile? I searched the archives but could not find information that explained this directly; apologies if this does already exist: if so, could you please point me towards it? Thank you so much for your help, Best wishes, Nela Nela Cicmil D.Phil Candidate, Neurophysiology Dept. Physiology, Anatomy Genetics University of Oxford Tel: 01865 282274 Internal: 82274 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] cortical surface of individual subject: coordinates in individual's MNI space
1. Yes, just apply the talairach.xfm transform to each vertex. Should be easy enough to do in matlab using read_surf.m. 2. Yes, this can also be done in matlab, saving either in curv (write_curv.m) or wfile format. On Sat, 22 Oct 2011, Nela Cicmil wrote: Dear Freesurfer Developers and Users, I have two question(s) about Freesurfer and individual subject's MNI coordinates: (1) Having run recon-all to reconstruct the cortical surface for an individual subject in my study, is it possible to obtain the list of coordinates that describe the points in the individual subject's MNI space that comprise the cortical surface of that subject's brain? This is in order to run an MEG beamformer analysis (in matlab) in the subject's own MNI space, but restricted to those voxels that comprise the cortical surface for that subject, as calculated by Freesurfer. (2) Once I have obtained (in matlab), for a list of voxels that comprise the cortical surface, each of the their MNI coordinates and their associated activation value (e.g. tstat), is there a straightforward way to display this on the cortical surface of that subject in tksurfer, for example by converting to a simple wfile? I searched the archives but could not find information that explained this directly; apologies if this does already exist: if so, could you please point me towards it? Thank you so much for your help, Best wishes, Nela Nela Cicmil D.Phil Candidate, Neurophysiology Dept. Physiology, Anatomy Genetics University of Oxford Tel: 01865 282274 Internal: 82274 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] cortical surface of individual subject: coordinates in individual's MNI space
Dear Freesurfer Developers and Users, I have two question(s) about Freesurfer and individual subject's MNI coordinates: (1) Having run recon-all to reconstruct the cortical surface for an individual subject in my study, is it possible to obtain the list of coordinates that describe the points in the individual subject's MNI space that comprise the cortical surface of that subject's brain? This is in order to run an MEG beamformer analysis (in matlab) in the subject's own MNI space, but restricted to those voxels that comprise the cortical surface for that subject, as calculated by Freesurfer. (2) Once I have obtained (in matlab), for a list of voxels that comprise the cortical surface, each of the their MNI coordinates and their associated activation value (e.g. tstat), is there a straightforward way to display this on the cortical surface of that subject in tksurfer, for example by converting to a simple wfile? I searched the archives but could not find information that explained this directly; apologies if this does already exist: if so, could you please point me towards it? Thank you so much for your help, Best wishes, Nela Nela Cicmil D.Phil Candidate, Neurophysiology Dept. Physiology, Anatomy Genetics University of Oxford Tel: 01865 282274 Internal: 82274 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] cortical surface areas
Hi, Is there a tool to derive the cortical surface areas of the cortical structures listed in aseg.stats? Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] cortical surface areas
Hi Ed, the surface areas are usually in the aparc files as they are functions of the surface models, while the aseg is a volume segmentation. cheers Bruce On Mon, 15 Nov 2010, Ed Gronenschild wrote: Hi, Is there a tool to derive the cortical surface areas of the cortical structures listed in aseg.stats? Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] cortical surface in MNI space?
Hi David, I use both the MINC world and the freesurfer world. One thing which may be of use to you or others, is to get from the surface co-ordinates, back to world-coordinates (or scanner RAS), so that minc tools etc. display things properly. To do this, you need to apply a simple translation. ie. for native.mnc which was your input into freesurfer do this command: mri_info --cras native.mnc my output was -2.35588 52.7907 24.8145 Then you can create the following transformation matrix: 1 0 0 -2.35588 0 1 0 52.7907 0 0 0 24.8145 0 0 0 1 If you then convert your surfaces to ascii: mris_convert lh.pial lh.pial.asc You can then transform each co-ordinate point in lh.pial.asc with the above transformation matrix and then your surfaces will be in MNI world co-cordinates. (these are referred to as scanner RAS on the freesurfer wiki coordinate page). From there, if you have a transformation that already maps your subject to mni152, then you can apply that transformation. I think annother way, would be to use the information provided in: $FREESURFER_HOME/average/mni152.register.dat. I'm assuming lines 5-9 of that file are a transformation that will move you from mni152 space to fsaverage (avg305) space. (though im not sure if that is moving you from a SurfaceRAS to SurfaceRAS space or just from RAS to RAS or what?) If FreeSurfer calculates the transformation matrix required to get from your subject space(native, or RAS, or SurfaceRAS) to fsaverage (RAS or SurfaceRAS) space, then you could probably combine those transformations to get what you want. Unfortunately, I don't have a good enough grasp of the coordinate system yet to guide you through this process. Perhaps Doug can guide me in the right direction? If you are interested in any of the other things, feel free to contact me as I have some tools to convert FreeSurfer outputs to MINC outputs (.mnc, .obj). hope that helps, mishkin On Mon, Apr 14, 2008 at 11:52 AM, Doug Greve [EMAIL PROTECTED] wrote: Rather than creating a subject in mni152 space, you can map your 152 data to our fsaverage (mni305) with $FREESURFER_HOME/average/mni152.register.dat, eg tkmedit fsaverage T1.mgz -overlay yourstats152.nii \ -overlay-reg $FREESURFER_HOME/average/mni152.register.dat or tksurfer fsaverage lh inflated -overlay yourstats152.nii \ -overlay-reg $FREESURFER_HOME/average/mni152.register.dat doug Stark, David Ernest wrote: Hi all, I am new to Freesurfer and would like to generate a cortical (pial) surface of 1 subject's brain, but I need the surface in MNI 152 space (this is for display purposes, so that I can overlay clusters already in MNI space). What is the best way to accomplish this? I already have the subject's freesurfed output (if any of those files can be of use). Also, if a pial surface already exists for one of the standard brains out there, that would also be of use. Thanks! David ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cortical surface in MNI space?
Rather than creating a subject in mni152 space, you can map your 152 data to our fsaverage (mni305) with $FREESURFER_HOME/average/mni152.register.dat, eg tkmedit fsaverage T1.mgz -overlay yourstats152.nii \ -overlay-reg $FREESURFER_HOME/average/mni152.register.dat or tksurfer fsaverage lh inflated -overlay yourstats152.nii \ -overlay-reg $FREESURFER_HOME/average/mni152.register.dat doug Stark, David Ernest wrote: Hi all, I am new to Freesurfer and would like to generate a cortical (pial) surface of 1 subject's brain, but I need the surface in MNI 152 space (this is for display purposes, so that I can overlay clusters already in MNI space). What is the best way to accomplish this? I already have the subject's freesurfed output (if any of those files can be of use). Also, if a pial surface already exists for one of the standard brains out there, that would also be of use. Thanks! David ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] cortical surface in MNI space?
Hi all, I am new to Freesurfer and would like to generate a cortical (pial) surface of 1 subject's brain, but I need the surface in MNI 152 space (this is for display purposes, so that I can overlay clusters already in MNI space). What is the best way to accomplish this? I already have the subject's freesurfed output (if any of those files can be of use). Also, if a pial surface already exists for one of the standard brains out there, that would also be of use. Thanks! David ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] cortical surface in MNI space?
Hi all, I am new to Freesurfer and would like to generate a cortical (pial) surface of 1 subject's brain, but I need the surface in MNI 152 space (this is for display purposes, so that I can overlay clusters already in MNI space). What is the best way to accomplish this? I already have the subject's freesurfed output (if any of those files can be of use). Also, if a pial surface already exists for one of the standard brains out there, that would also be of use. Thanks! David ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cortical surface contour plotting
tkmedit finds ever triangle that intersects the viewing plane then computes the closed contour connecting them. Is that what you want? Bruce On Fri, 19 Oct 2007, XJ Kang wrote: Hi, I can get all the ponits of the cortical surface in ascii format. Anyway I can plot the contour of the 3D surface on a plane? I tried to find all the points in one plane, but the order is not along the contour line. I can only plot the surface as dots, instead of lines in a 2D plane. I am wonderng how tkmedit plots the surface lines. Any freesurfer function can do this? Thanks. XJ Kang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Cortical surface contour plotting
Hi, I can get all the ponits of the cortical surface in ascii format. Anyway I can plot the contour of the 3D surface on a plane? I tried to find all the points in one plane, but the order is not along the contour line. I can only plot the surface as dots, instead of lines in a 2D plane. I am wonderng how tkmedit plots the surface lines. Any freesurfer function can do this? Thanks. XJ Kang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Cortical surface tessellation and smoothing
Dear list, Is there a paper or any documentation describing how freesurfer tessellate and smooth cortical surfaces? In particular, does freesurfer use any specific variety of marching cube isosurface algorithm? Regular surface smoothing (like the Laplacian smoothing) may cause undesired surface shrinking. It looks that freesurfer does a good job on surface smothing. So I'm wondering what smoothing algorithm freesurfer employ. Thanks, Kai ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cortical surface tessellation and smoothing
Hi Kai, it was described in the Dale, et al. 1999 paper in NeuroImage, or maybe part in that and part in the 2nd part of it (Fischl et al., 1999 also NeuroImage). They are both on our wiki (surfer.nmr.mgh.harvard.edu/fswiki). We don't use marching cubes, but a custom tesselation algorithm. The surface smoothing is like a Laplacian, but the surface area of the inflated surface is constrained to be the same as the original surface. cheers, Bruce On Mon, 25 Jun 2007, Kai Li wrote: Dear list, Is there a paper or any documentation describing how freesurfer tessellate and smooth cortical surfaces? In particular, does freesurfer use any specific variety of marching cube isosurface algorithm? Regular surface smoothing (like the Laplacian smoothing) may cause undesired surface shrinking. It looks that freesurfer does a good job on surface smothing. So I'm wondering what smoothing algorithm freesurfer employ. Thanks, Kai ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cortical surface measurement.
yes, you can manually draw them in tksurfer, save them as a label file, then specify the label with -l label file name to mris_anatomical_stats. cheers, Bruce On Wed, 19 Apr 2006, Goradia, Dhruman D wrote: Hello All, Is it possible to find ROI based cortical surface measures using freesurfer? I am interested in manually tracing ROI and then obtaining thickness, surface area and curvature measures for the ROI. Is there a way to do this in freesurfer? Thank you -Dhruman ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
