Hello Bruce and All,
Here are some new questions to an ongoing issue.
1. What are advantages of version 5.0 over the former version? I have processed 82 scans so far in the former version and am debating whether to re-run them all in 5.0. We will eventually have a total of 560 scans, so we need to decide soon.
2. In version 5.0, when I run
tksurfer $i lh pial -annotation aparc
the corpus callossum is labeled as "none". Is there a way to have it be labeled correctly as itself in ver 5?
Thanks, Helen
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Helen,
the Release Notes page describes the differences between versions:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
but more importantly, we will be releasing a new version, v5.1, within the next couple weeks. primarily the big difference between 5.1 and 4.5 are improvements to the longitudinal stream.
per your corpus callossum question, that was removed in the 5.0 version, as it never really belonged as a surface parcellation. its volume measure is found in the aseg.
n.
On Mon, 2011-03-07 at 15:16 +0000, Keefe, Helen L wrote:
Hello Bruce and All,
Here are some new questions to an ongoing issue.
- What are advantages of version 5.0 over the former version? I
have processed 82 scans so far in the former version and am debating whether to re-run them all in 5.0. We will eventually have a total of 560 scans, so we need to decide soon.
- In version 5.0, when I run
tksurfer $i lh pial -annotation aparc
the corpus callossum is labeled as "none". Is there a way to have it be labeled correctly as itself in ver 5?
Thanks, Helen
Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ______________________________________________________________________ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello,
We try to look at the two group difference of cortical thickness, but I need the lh(or rh).thickness file, which reported in template space (FS average space), but after run recon-all -all, what I have is only lh.thickness, or rh.thickness, which is in subject's space. Would someone point me where or how I can get them? Thanks.
Aize
Aize,
run:
recon-all -s subjid -qcache -measure thickness
and this will create files in the /surf dir which sample the thickness data at different smoothing levels onto the fsaverage subject space.
n.
On Wed, 2011-03-09 at 05:46 +0800, caoaize wrote:
Hello,
We try to look at the two group difference of cortical thickness, but I need the lh(or rh).thickness file, which reported in template space (FS average space), but after run recon-all -all, what I have is only lh.thickness, or rh.thickness, which is in subject's space. Would someone point me where or how I can get them? Thanks.
Aize
Hello there, We have a bunch of files that had freesurfer run already, simply using the command "recon-all -s subjid -all", in order to get the cortical thickness in fs average space, should we have to re-run all of them again using "recon-all -s subjid -qcache -measure thickness", or we may apply some transformation reported already to transform the thickness from subject space to fs average space ? Does anyone have any suggestion on how to do that? Thanks. Aize
Subject: Re: Cortical thickness in the template space From: nicks@nmr.mgh.harvard.edu To: caoaize@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Date: Tue, 8 Mar 2011 16:50:41 -0500
Aize,
run:
recon-all -s subjid -qcache -measure thickness
and this will create files in the /surf dir which sample the thickness data at different smoothing levels onto the fsaverage subject space.
n.
On Wed, 2011-03-09 at 05:46 +0800, caoaize wrote:
Hello,
We try to look at the two group difference of cortical thickness, but I need the lh(or rh).thickness file, which reported in template space (FS average space), but after run recon-all -all, what I have is only lh.thickness, or rh.thickness, which is in subject's space. Would someone point me where or how I can get them? Thanks.
Aize
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.
Hi Aize,
yes, that should do it.
cheers, Bruce On Fri, 15 Apr 2011, caoaize wrote:
Hello there, We have a bunch of files that had freesurfer run already, simply using the command "recon-all -s subjid -all", in order to get the cortical thickness in fs average space, should we have to re-run all of them again using "recon-all -s subjid -qcache -measure thickness", or we may apply some transformation reported already to transform the thickness from subject space to fs average space ? Does anyone have any suggestion on how to do that? Thanks. Aize
Subject: Re: Cortical thickness in the template space From: nicks@nmr.mgh.harvard.edu To: caoaize@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Date: Tue, 8 Mar 2011 16:50:41 -0500
Aize,
run:
recon-all -s subjid -qcache -measure thickness
and this will create files in the /surf dir which sample the thickness data at different smoothing levels onto the fsaverage subject space.
n.
On Wed, 2011-03-09 at 05:46 +0800, caoaize wrote:
Hello,
We try to look at the two group difference of cortical thickness, but I need the lh(or rh).thickness file, which reported in template space (FS average space), but after run recon-all -all, what I have is only lh.thickness, or rh.thickness, which is in subject's space. Would someone point me where or how I can get them? Thanks.
Aize
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.
Hi, Bruce, I realized that I should use mris_sphere, mris_register and mrisp_paint tools, but I have no idea on how to set the parameters of these commands. May you or somebody else give me some help? Thanks. Aize
Date: Fri, 15 Apr 2011 10:47:08 -0400 From: fischl@nmr.mgh.harvard.edu To: caoaize@hotmail.com CC: nicks@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cortical thickness in the template space
Hi Aize,
yes, that should do it.
cheers, Bruce On Fri, 15 Apr 2011, caoaize wrote:
Hello there, We have a bunch of files that had freesurfer run already, simply using the command "recon-all -s subjid -all", in order to get the cortical thickness in fs average space, should we have to re-run all of them again using "recon-all -s subjid -qcache -measure thickness", or we may apply some transformation reported already to transform the thickness from subject space to fs average space ? Does anyone have any suggestion on how to do that? Thanks. Aize
Subject: Re: Cortical thickness in the template space From: nicks@nmr.mgh.harvard.edu To: caoaize@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Date: Tue, 8 Mar 2011 16:50:41 -0500
Aize,
run:
recon-all -s subjid -qcache -measure thickness
and this will create files in the /surf dir which sample the thickness data at different smoothing levels onto the fsaverage subject space.
n.
On Wed, 2011-03-09 at 05:46 +0800, caoaize wrote:
Hello,
We try to look at the two group difference of cortical thickness, but I need the lh(or rh).thickness file, which reported in template space (FS average space), but after run recon-all -all, what I have is only lh.thickness, or rh.thickness, which is in subject's space. Would someone point me where or how I can get them? Thanks.
Aize
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.
Hi Aize
-qcache -measure thickness should do everything you want
cheers Bruce
On Fri, 15 Apr 2011, caoaize wrote:
Hi, Bruce, I realized that I should use mris_sphere, mris_register and mrisp_paint tools, but I have no idea on how to set the parameters of these commands. May you or somebody else give me some help? Thanks. Aize
Date: Fri, 15 Apr 2011 10:47:08 -0400 From: fischl@nmr.mgh.harvard.edu To: caoaize@hotmail.com CC: nicks@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cortical thickness in the template space
Hi Aize,
yes, that should do it.
cheers, Bruce On Fri, 15 Apr 2011, caoaize wrote:
Hello there, We have a bunch of files that had freesurfer run already, simply using the command "recon-all -s subjid -all", in order to get the cortical thickness in fs average space, should we have to re-run all of them again using "recon-all -s subjid -qcache -measure thickness", or we may apply some transformation reported already to transform the thickness from subject space to fs average space ? Does anyone have any suggestion on how to do that? Thanks. Aize
Subject: Re: Cortical thickness in the template space From: nicks@nmr.mgh.harvard.edu To: caoaize@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Date: Tue, 8 Mar 2011 16:50:41 -0500
Aize,
run:
recon-all -s subjid -qcache -measure thickness
and this will create files in the /surf dir which sample the thickness data at different smoothing levels onto the fsaverage subject space.
n.
On Wed, 2011-03-09 at 05:46 +0800, caoaize wrote:
Hello,
We try to look at the two group difference of cortical thickness, but I need the lh(or rh).thickness file, which reported in template space (FS average space), but after run recon-all -all, what I have is only lh.thickness, or rh.thickness, which is in subject's space. Would someone point me where or how I can get them? Thanks.
Aize
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@nmr.mgh.harvard.edu
-
Bruce Fischl -
caoaize -
Keefe, Helen L -
Nick Schmansky