Re: [Freesurfer] Cortical surface analysis

2021-04-28 Thread Fischl, Bruce 
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


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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>>
 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


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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>>
 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


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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>>
 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


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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,

Re: [Freesurfer] Cortical surface analysis

2021-04-28 Thread Ornaith O Reilly 
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 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?

Re: [Freesurfer] Freeview slow on CentOS 8 Stream

2021-04-28 Thread Torkil Svensgaard 
External Email - Use Caution

Hi

We've moved to an environment modules setup for the new HPC installation 
and I've made modules for 5.3.0, 6.0.0 and 7.1.1, which all exhibit the 
same symptom.

I installed a dev build this morning and one heavy user reports the 
following from working with it:

"
I used freeview heavily during the day and it worked fine.

Now logged on again (with the same viewer open) and it was impossible to 
work with.

Even killing it takes forever, and after the window disappears the 
terminal is still working on something.

Had to also kill the terminal.
"

We run Thinlinc as thin client point of entry, freeview is run directly 
on the login nodes which are fairly beefy things with 256GB RAM.

Mvh.

Torkil

On 27/04/2021 23.12, fsbuild wrote:
>  External Email - Use Caution
> 
> Hello Torkil,
> 
> Not sure what version of Freesurfer you are using, but if it’s an older 
> release, it could be interesting to compare the performance with one of 
> the latest development builds (not a release) from *MailScanner has 
> detected a possible fraud attempt from "secure-web.cisco.com" claiming 
> to be* 
> https://secure-web.cisco.com/1fCfSGPn1qXkEuvvvBRvaI4Ptbc4Y_VDhBATIsjsDTPCsUKGA68wpQ8QSGMyRuo5dqi6WKrzNk6CWEv3D3k5zgXwVSeUnKbeRMfUPHhP2dywnvdWawfc6hGOU366WlwqrUw9FCRjGeAGc_UxVQOnlVLyo87p5nMa74RlG4twGiXMh54wvDjvt3bRL7G8veAW6UWxddG2PU7QmbmDWGcL0QqQI3v5R4stApLAKQ6b48qDeL3LJC3ZwIR9FbXqj-73ujzq3nj8oO_e1uGuON87bFQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2F
>  
> .
>  
>   There’s an archive and RPM for CentOS7 and an archive for a CentOS8 build.
> 
> - R.
> 
>> On Apr 27, 2021, at 04:18, Torkil Svensgaard  wrote:
>>
>>    External Email - Use Caution
>>
>> Hi Ruopeng
>>
>> The users all agree it is GUI responsiveness. Everything else can run
>> just stellar on the very same desktop, matlab etc, at the same time as
>> freeview stalls.
>>
>> Mvh.
>>
>> Torkil
>>
>> On 26/04/2021 19.16, Wang, Ruopeng wrote:
>>> Hi Torkil,
>>>
>>> Can you tell what part of the program slows down the most? Data 
>>> loading? GUI responsiveness? Image/3D rendering? Or just in general? 
>>> If it is the rendering, maybe try updating the graphics card driver 
>>> to the latest?
>>>
>>> Best,
>>> Ruopeng
>>>
 On Apr 26, 2021, at 6:06 AM, Torkil Svensgaard  wrote:

    External Email - Use Caution

 Hi

 We have an older Ubuntu 16.04 HPC installation on which Freeview runs
 just fine. We also have a brand new CentOS 8 Stream HPC installation
 with much better hardware on which Freeview slows to a crawl after a bit
 of use.

 There's no error as such, it just slows to the point of being unusable.

 Any suggestions on how to fix it, or pinpoint the cause?

 Thanks,

 Torkil


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[Freesurfer] Cannot select ROI edit tool in Freeview

2021-04-28 Thread Mercy Mazurek 
External Email - Use Caution

I loaded my brainmask.mgz file generated from a "recon-all -autorecon1"
command. When I open up Freeview, I see the icon but it is grayed out and I
cannot select it to create a volume ROI on my image. How do I draw an ROI
on my scans?

Thanks for your help!
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