Hi,
We're trying to edit the aseg segmentation and reconstruct it. If we run 'recon-all -s subject -make all' does that depend on any information from the surfaces or brainmask volume, or are the stats independent of that?
Thank you,
Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia
Hi Jordan, I'm not sure I understand your question. If you run -make all, it will run recon-all again starting at the earliest step in which there are files that were changed that affect that step. It will run all the way through to the end as each step affects the next one. This will change your stats which are produced in autorecon3. Allison
On Apr 16, 2012, at 10:28 AM, Jordan Pierce jepierce87@yahoo.com wrote:
Hi,
We're trying to edit the aseg segmentation and reconstruct it. If we run 'recon-all -s subject -make all' does that depend on any information from the surfaces or brainmask volume, or are the stats independent of that?
Thank you,
Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Is there a way to only get the stats from the -aseg file that we edited without rebuilding everything? For example, I edited a subject yesterday and ran the -make all option, but the reconstruction changed everything in -aseg so cerebellum is marked as grey and white matter (see attached). Do we just have keep repeating this step until it gets it right?
Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia
________________________________ From: Allison Stevens Player astevens@nmr.mgh.harvard.edu To: Jordan Pierce jepierce87@yahoo.com Cc: Freesurfer Support freesurfer@nmr.mgh.harvard.edu Sent: Monday, April 16, 2012 3:21 PM Subject: Re: [Freesurfer] Segmentation
Hi Jordan, I'm not sure I understand your question. If you run -make all, it will run recon-all again starting at the earliest step in which there are files that were changed that affect that step. It will run all the way through to the end as each step affects the next one. This will change your stats which are produced in autorecon3. Allison
On Apr 16, 2012, at 10:28 AM, Jordan Pierce jepierce87@yahoo.com wrote:
Hi,
We're trying to edit the aseg segmentation and reconstruct it. If we run 'recon-all -s subject -make all' does that depend on any information from the surfaces or brainmask volume, or are the stats independent of that?
Thank you, Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia
_______________________________________________
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Hi Jordan That's pretty bad and means something's went radically wrong pretty early in the process. Have you checked the talairach.lta?
Cheers Bruce
On Apr 17, 2012, at 8:31 AM, Jordan Pierce jepierce87@yahoo.com wrote:
Is there a way to only get the stats from the -aseg file that we edited without rebuilding everything? For example, I edited a subject yesterday and ran the -make all option, but the reconstruction changed everything in -aseg so cerebellum is marked as grey and white matter (see attached). Do we just have keep repeating this step until it gets it right?
Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia From: Allison Stevens Player astevens@nmr.mgh.harvard.edu To: Jordan Pierce jepierce87@yahoo.com Cc: Freesurfer Support freesurfer@nmr.mgh.harvard.edu Sent: Monday, April 16, 2012 3:21 PM Subject: Re: [Freesurfer] Segmentation
Hi Jordan, I'm not sure I understand your question. If you run -make all, it will run recon-all again starting at the earliest step in which there are files that were changed that affect that step. It will run all the way through to the end as each step affects the next one. This will change your stats which are produced in autorecon3. Allison
On Apr 16, 2012, at 10:28 AM, Jordan Pierce jepierce87@yahoo.com wrote:
Hi,
We're trying to edit the aseg segmentation and reconstruct it. If we run 'recon-all -s subject -make all' does that depend on any information from the surfaces or brainmask volume, or are the stats independent of that?
Thank you,
Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia _______________________________________________ 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.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
What should I be looking for in the talairach.lta?
Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia
________________________________ From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Jordan Pierce jepierce87@yahoo.com Cc: Allison Stevens Player astevens@nmr.mgh.harvard.edu; Freesurfer Support freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, April 17, 2012 9:37 AM Subject: Re: [Freesurfer] Segmentation
Hi Jordan That's pretty bad and means something's went radically wrong pretty early in the process. Have you checked the talairach.lta?
Cheers Bruce
On Apr 17, 2012, at 8:31 AM, Jordan Pierce jepierce87@yahoo.com wrote:
Is there a way to only get the stats from the -aseg file that we edited without rebuilding everything? For example, I edited a subject yesterday and ran the -make all option, but the reconstruction changed everything in -aseg so cerebellum is marked as grey and white matter (see attached). Do we just have keep repeating this step until it gets it right?
Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia
From: Allison Stevens Player astevens@nmr.mgh.harvard.edu To: Jordan Pierce jepierce87@yahoo.com Cc: Freesurfer Support freesurfer@nmr.mgh.harvard.edu Sent: Monday, April 16, 2012 3:21 PM Subject: Re: [Freesurfer] Segmentation
Hi Jordan, I'm not sure I understand your question. If you run -make all, it will run recon-all again starting at the earliest step in which there are files that were changed that affect that step. It will run all the way through to the end as each step affects the next one. This will change your stats which are produced in autorecon3. Allison
On Apr 16, 2012, at 10:28 AM, Jordan Pierce jepierce87@yahoo.com wrote:
Hi,
We're trying to edit the aseg segmentation and reconstruct it. If we run 'recon-all -s subject -make all' does that depend on any information from the surfaces or brainmask volume, or are the stats independent of that?
Thank you, Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia
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.png> _______________________________________________
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You can check it with: cd $SUBJECTS_DIR/$subject/mri tkregister2 --mov $FREESURFER_HOME/average/RB_all_2008-03-26.gca --targ brainmask.mgz --lta-inv transforms/talairach.lta --reg junk.reg.dat --s $subject
don't try to edit it though. If it is off, get back to us. doug
On 04/17/2012 12:08 PM, Jordan Pierce wrote:
What should I be looking for in the talairach.lta? Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia *From:* Bruce Fischl fischl@nmr.mgh.harvard.edu *To:* Jordan Pierce jepierce87@yahoo.com *Cc:* Allison Stevens Player astevens@nmr.mgh.harvard.edu; Freesurfer Support freesurfer@nmr.mgh.harvard.edu *Sent:* Tuesday, April 17, 2012 9:37 AM *Subject:* Re: [Freesurfer] Segmentation
Hi Jordan That's pretty bad and means something's went radically wrong pretty early in the process. Have you checked the talairach.lta?
Cheers Bruce
On Apr 17, 2012, at 8:31 AM, Jordan Pierce <jepierce87@yahoo.com mailto:jepierce87@yahoo.com> wrote:
Is there a way to only get the stats from the -aseg file that we edited without rebuilding everything? For example, I edited a subject yesterday and ran the -make all option, but the reconstruction changed everything in -aseg so cerebellum is marked as grey and white matter (see attached). Do we just have keep repeating this step until it gets it right? Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia *From:* Allison Stevens Player <astevens@nmr.mgh.harvard.edu mailto:astevens@nmr.mgh.harvard.edu> *To:* Jordan Pierce <jepierce87@yahoo.com mailto:jepierce87@yahoo.com> *Cc:* Freesurfer Support <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> *Sent:* Monday, April 16, 2012 3:21 PM *Subject:* Re: [Freesurfer] Segmentation
Hi Jordan, I'm not sure I understand your question. If you run -make all, it will run recon-all again starting at the earliest step in which there are files that were changed that affect that step. It will run all the way through to the end as each step affects the next one. This will change your stats which are produced in autorecon3. Allison
On Apr 16, 2012, at 10:28 AM, Jordan Pierce <jepierce87@yahoo.com mailto:jepierce87@yahoo.com> wrote:
Hi,
We're trying to edit the aseg segmentation and reconstruct it. If we run 'recon-all -s subject -make all' does that depend on any information from the surfaces or brainmask volume, or are the stats independent of that?
Thank you, Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia _______________________________________________ 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.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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
I've attached an image of the talairach.lta, which does seem to have taken a chunk out of the back of the brain. Is this what affects the cerebellum issues? I assume we should check this for every subject and correct it manually if necessary, but I'm confused as to how this missing chunk does not show a problem in the brainmask.mgz. There seem to be a lot of steps and files built automatically that build on each other, and many places for things to go wrong so it's hard to tell where to look first.
Thanks for your help,
Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia
________________________________ From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Jordan Pierce jepierce87@yahoo.com Cc: Allison Stevens Player astevens@nmr.mgh.harvard.edu; Freesurfer Support freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, April 17, 2012 9:37 AM Subject: Re: [Freesurfer] Segmentation
Hi Jordan That's pretty bad and means something's went radically wrong pretty early in the process. Have you checked the talairach.lta?
Cheers Bruce
On Apr 17, 2012, at 8:31 AM, Jordan Pierce jepierce87@yahoo.com wrote:
Is there a way to only get the stats from the -aseg file that we edited without rebuilding everything? For example, I edited a subject yesterday and ran the -make all option, but the reconstruction changed everything in -aseg so cerebellum is marked as grey and white matter (see attached). Do we just have keep repeating this step until it gets it right?
Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia
From: Allison Stevens Player astevens@nmr.mgh.harvard.edu To: Jordan Pierce jepierce87@yahoo.com Cc: Freesurfer Support freesurfer@nmr.mgh.harvard.edu Sent: Monday, April 16, 2012 3:21 PM Subject: Re: [Freesurfer] Segmentation
Hi Jordan, I'm not sure I understand your question. If you run -make all, it will run recon-all again starting at the earliest step in which there are files that were changed that affect that step. It will run all the way through to the end as each step affects the next one. This will change your stats which are produced in autorecon3. Allison
On Apr 16, 2012, at 10:28 AM, Jordan Pierce jepierce87@yahoo.com wrote:
Hi,
We're trying to edit the aseg segmentation and reconstruct it. If we run 'recon-all -s subject -make all' does that depend on any information from the surfaces or brainmask volume, or are the stats independent of that?
Thank you, Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia
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.png> _______________________________________________
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
Jordan Pierce