I've never done it in FS, but you might be able to do it with
mris_convert using -c option and specifying a gifti as an output
On 2/1/2021 8:19 PM, Sam W wrote:
External Email - Use Caution
Hi!
Just pinging. Is there a way to get the surface+overlay file as
mentioned above using freesurfer? Thank you!
Best regards,
Sam
---------- Forwarded message ---------
From: *Sam W* <samf...@gmail.com <mailto:samf...@gmail.com>>
Date: Fri, Jul 10, 2020 at 9:05 PM
Subject: Re: [Freesurfer] label to surface
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Hi Doug and Tim,
I'm running probtrackx with freesurfer surfaces as seeds. However
probtrackx requires a file that contains both the whole surface file
(eg, lh.pial) as well as the overlay (the scalar values associated
with the vertices of the roi).
I can create such a file with FSL's label2surf command which creates a
gifti file that encodes both the surface and the overlay.
My question is whether I can do the same with freesurfer? Running
probtrackx with the overlay from mri_label2label --outmask does not
work. It also needs the associated pial or white surface.
Best regards,
Sam
On Fri, Jul 10, 2020 at 4:29 PM Douglas N. Greve
<dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote:
what do you mean merge with the pial?
On 7/9/2020 8:07 PM, Sam W wrote:
External Email - Use Caution
It works great Doug, thanks a lot!
Can I ask you a follow up question please? I created the overlay
with mri_label2label using --outmask as you suggested, but now
I'd like to merge that overlay with the pial surface (lh.pial).
Is there a tool I can use to achieve that result?
Best regards,
Sam
On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve
<dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote:
Use mri_label2label with the --outmask option
On 7/8/2020 10:14 PM, Sam W wrote:
External Email - Use Caution
Hi,
Is there a way to convert a label file into a
surface/overlay? Thank you!
Best regards,
Sam
_______________________________________________
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/14Le9F02YSqeepBlENPo9ukq6i4TYc7zAHc-GwEnBTCPsLMW-ksg83S9TsBRlTTTfp41tpf009gzFnQ_H__V-4VIo_7E5lXSfrrsM_V9q8Xwy5nfXyAu1OV-ZHwwsvohy4LQk0ZHbtgAUlaj_l1Zxv2xxI4TqSGtD2iTjFEll2fSIZn3hEWtZEBkM_rv-hQscN6_6VLxq8XxTPuTbC_PdtEcuFJhEKdxlcqTzynCaRegvb68Zn54YpLBpqN8fc6_uLZQ_IiAUHwQow-_FmIiIDQ/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/14Le9F02YSqeepBlENPo9ukq6i4TYc7zAHc-GwEnBTCPsLMW-ksg83S9TsBRlTTTfp41tpf009gzFnQ_H__V-4VIo_7E5lXSfrrsM_V9q8Xwy5nfXyAu1OV-ZHwwsvohy4LQk0ZHbtgAUlaj_l1Zxv2xxI4TqSGtD2iTjFEll2fSIZn3hEWtZEBkM_rv-hQscN6_6VLxq8XxTPuTbC_PdtEcuFJhEKdxlcqTzynCaRegvb68Zn54YpLBpqN8fc6_uLZQ_IiAUHwQow-_FmIiIDQ/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/14Le9F02YSqeepBlENPo9ukq6i4TYc7zAHc-GwEnBTCPsLMW-ksg83S9TsBRlTTTfp41tpf009gzFnQ_H__V-4VIo_7E5lXSfrrsM_V9q8Xwy5nfXyAu1OV-ZHwwsvohy4LQk0ZHbtgAUlaj_l1Zxv2xxI4TqSGtD2iTjFEll2fSIZn3hEWtZEBkM_rv-hQscN6_6VLxq8XxTPuTbC_PdtEcuFJhEKdxlcqTzynCaRegvb68Zn54YpLBpqN8fc6_uLZQ_IiAUHwQow-_FmIiIDQ/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/14Le9F02YSqeepBlENPo9ukq6i4TYc7zAHc-GwEnBTCPsLMW-ksg83S9TsBRlTTTfp41tpf009gzFnQ_H__V-4VIo_7E5lXSfrrsM_V9q8Xwy5nfXyAu1OV-ZHwwsvohy4LQk0ZHbtgAUlaj_l1Zxv2xxI4TqSGtD2iTjFEll2fSIZn3hEWtZEBkM_rv-hQscN6_6VLxq8XxTPuTbC_PdtEcuFJhEKdxlcqTzynCaRegvb68Zn54YpLBpqN8fc6_uLZQ_IiAUHwQow-_FmIiIDQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
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
