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
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Ornaith O Reilly
*Sent:* Wednesday, April 28, 2021 4:30 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*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 <bfis...@mgh.harvard.edu
<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>
<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 <freesurfer@nmr.mgh.harvard.edu
<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
<bfis...@mgh.harvard.edu <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>
<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 <freesurfer@nmr.mgh.harvard.edu
<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
<bfis...@mgh.harvard.edu <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>
<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
<freesurfer@nmr.mgh.harvard.edu
<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
<dgr...@mgh.harvard.edu <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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
*MailScanner has detected a possible fraud attempt
from "secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://secure-web.cisco.com/1Ogp5ZeoS72_H9fgRPteNOma_J9hPaTfdzd6HC3IGubCY3vT-6900ngXdEssiUKOEN83iJbaRuxNMiShdLlOKXEsjibjQ3746iu4iSesiMAO7FM0u9JNkAiZ3RbN0TT8aAzo0QUe3wE1wLOfCaW_LV58ZUFvu4Jp8VcRYtLlFq2jaZ4IhvfVwk9EAHZ2f2uNFvgXVQwrjI8lddgCE_MHRU2_3rGmlnYXAhqWlm22ouXXjaE7nx7oKhyinkx8WQ1Qz1t7wnWmQku8NFdH3eu0s6Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
*MailScanner has detected a possible fraud attempt
from "secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://secure-web.cisco.com/1Ogp5ZeoS72_H9fgRPteNOma_J9hPaTfdzd6HC3IGubCY3vT-6900ngXdEssiUKOEN83iJbaRuxNMiShdLlOKXEsjibjQ3746iu4iSesiMAO7FM0u9JNkAiZ3RbN0TT8aAzo0QUe3wE1wLOfCaW_LV58ZUFvu4Jp8VcRYtLlFq2jaZ4IhvfVwk9EAHZ2f2uNFvgXVQwrjI8lddgCE_MHRU2_3rGmlnYXAhqWlm22ouXXjaE7nx7oKhyinkx8WQ1Qz1t7wnWmQku8NFdH3eu0s6Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://secure-web.cisco.com/1I1PNb10uTGevPjzK0_T5DjLYdNQpKw1HSsrVrnYZ179WEfRQ3IE3szslsovY-jgkoHTqK-F4hR4siQ2rXJRA0bVvDKJQEG-Kn2GAI1heNKJstATEXkJ3p1JpRqpCKLD2I1jPOw0AYWGn4ThpEi7I7Ro0ZwbONrs6pLnGS3349Q08FQR_wRQc6N9K0cKlSk-3_nXkU8A4QBVAQ5Nl_bqBQLexDtLtQMPe-5AamZPdQthNg8TG76tFXSpTfiCPb5p5jkLyq59Fsa80tlywx0otdQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://secure-web.cisco.com/13ECTorDkrsZkgjOR4TbCDCZexEsobOqsWP3xqIQ214KaFnTWJaqg68mt4-WOTImkHPkg1HO21XQxIFtFtdUxBAtYIauxEGnAlfGSHeHz3TPNSfBzEk72Q1o6y1dUQmAxC88ONKwSOXsymq-quqwLS5R_zOR2Om28eoryjL9q_ubptZdxBjZSJVZwSQ36viKvNhc-0OrhjNRBz5R_za6zhTSHSInIGAPywDBzFREGHAswbWu3MD2YBK5CTKlDDOpBZEJMhfHuPP7RNY529daoyA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://secure-web.cisco.com/13CuBIz-S54TcK37-KEXN52-oy09FZjKhFbCvS6Uovkwie8JDSNv0SHxDiJnD818B6imUf4UU3orR4Ftt7QIZtuhRXcDilXvivXy9NRFT1idB29UYw4UqjUL07nKGt1RsY0Gb9b9IvH__iZMyaXumIi538Ui_L6N72YRKeXbHAqoZ-10n7hpP0EhARunZjo5gjR3bAOaKszPmb8l32tg8JN4TTj6_z1UIEnYFbIebsymMOyWA7uD4xqeHvVr37I2rjG2jO2PcyT-Uf7GButBrVQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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 Mass General Brigham Compliance HelpLine at
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
http://www.massgeneralbrigham.org/complianceline
<http://secure-web.cisco.com/1DAaZOUd_lRWLZU0VyrgmxArDzAEZspdzTDa2TCz4M3FB17O8v_2hCQJTwZ5RURwS3GvwakeLxHAVybg2SBmpO0MlWRXwmhG2j8uqwiLDmK_NJ7KRYy2HM8srouGVBeV66XyN7oR8L-HcZMFKeKroeIJnqSx4rOhB27D2Vt87gzXImYluaojWkxyj_cvYbLMRaFSCOuKtR_VxY3zq7IPxhI0UB6IubKp3t1tHeFgfotJ-bsjebXlgthKQAxV-YTuADeXR4amUtp9K9Knw9DE5Vw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
. 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.
Please note that this e-mail is not secure (encrypted). If you do
not wish to continue communication over unencrypted e-mail, please
notify the sender of this message immediately. Continuing to send
or respond to e-mail after receiving this message means you
understand and accept this risk and wish to continue to
communicate over unencrypted e-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 Mass General Brigham
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
