Thanks Allison,
So to be clear, I just need to rename talairach.auto.xfm as talairach.xfm and then rerun recon-all from the normalization step? However, I'm not sure how to run recon starting from the normalization stage. Would you be able to help with that?
Also, I've been doing manual edits to the brain extraction as well as adding control points on all of my subjects and I'm wondering if this will negate any edits I've made. So I'm pretty much starting from scratch?
Thanks so much for looking into this for me!
Best, Krista
On Mon, Oct 7, 2013 at 12:19 PM, Allison Stevens < astevens@nmr.mgh.harvard.edu> wrote:
Hi Krista, I took a look at your subject and think I have determined the problem. Because your input data was high resolution (1.0000 x 0.9375 x 0.9375), the talairach registration step failed. If you look at the talairach.xfm, you'll see it is way off: tkregister2 --mgz --s BV20_2ndrun --fstal --surf orig
But the talairach.auto.xfm is correct. You can copy the talairach.auto.xfm to talairach.xfm and rerun from the -normalization step.
You might also want to look at these instructions: https://surfer.nmr.mgh.**harvard.edu/fswiki/HiResReconhttps://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon
They might not all apply to you but could potentially. Allison
---------- Forwarded message ----------
Date: Thu, 03 Oct 13 22:55:12 -0400 From: krista.kelly16@gmail.com To: fischl@nmr.mgh.harvard.edu Subject: V1 Labels
Hey!
Krista (krista.kelly16@gmail.com) has uploaded some files for you at the Martinos Center FileDrop:
-> BV20_2ndrun.zip (167.53 MiB) <http://gate.nmr.mgh.harvard.** edu/filedrop2/?u=1079qbdf&f=**dzep9n4http://gate.nmr.mgh.harvard.edu/filedrop2/?u=1079qbdf&f=dzep9n4
Also, they left this message for you: Hi Bruce,
Here is a zipped file of one of the subjects that I'm having label troubles with. The lh.v1.label isn't mapping correctly. I find the same goes for the aparc atlas as well (I haven't checked out anything else). If you could help me figure out why this is happening, that would be great!
Thanks, Krista
Please be aware, your upload will expire on December 31st. If you'd like to download these files, feel free to use the link below:
http://gate.nmr.mgh.harvard.**edu/filedrop2/?u=1079qbdfhttp://gate.nmr.mgh.harvard.edu/filedrop2/?u=1079qbdf
Cheers, The NMR Team
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/**compliancelinehttp://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.
Also, just to add to this, if I rerun recon in 5.1 starting from the normalization stage when I initially ran all subjects in 5.0, will this be a problem?
On Wed, Oct 9, 2013 at 8:05 PM, krista kelly krista.kelly16@gmail.comwrote:
Thanks Allison,
So to be clear, I just need to rename talairach.auto.xfm as talairach.xfm and then rerun recon-all from the normalization step? However, I'm not sure how to run recon starting from the normalization stage. Would you be able to help with that?
Also, I've been doing manual edits to the brain extraction as well as adding control points on all of my subjects and I'm wondering if this will negate any edits I've made. So I'm pretty much starting from scratch?
Thanks so much for looking into this for me!
Best, Krista
On Mon, Oct 7, 2013 at 12:19 PM, Allison Stevens < astevens@nmr.mgh.harvard.edu> wrote:
Hi Krista, I took a look at your subject and think I have determined the problem. Because your input data was high resolution (1.0000 x 0.9375 x 0.9375), the talairach registration step failed. If you look at the talairach.xfm, you'll see it is way off: tkregister2 --mgz --s BV20_2ndrun --fstal --surf orig
But the talairach.auto.xfm is correct. You can copy the talairach.auto.xfm to talairach.xfm and rerun from the -normalization step.
You might also want to look at these instructions: https://surfer.nmr.mgh.**harvard.edu/fswiki/HiResReconhttps://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon
They might not all apply to you but could potentially. Allison
---------- Forwarded message ----------
Date: Thu, 03 Oct 13 22:55:12 -0400 From: krista.kelly16@gmail.com To: fischl@nmr.mgh.harvard.edu Subject: V1 Labels
Hey!
Krista (krista.kelly16@gmail.com) has uploaded some files for you at the Martinos Center FileDrop:
-> BV20_2ndrun.zip (167.53 MiB) <http://gate.nmr.mgh.harvard.** edu/filedrop2/?u=1079qbdf&f=**dzep9n4http://gate.nmr.mgh.harvard.edu/filedrop2/?u=1079qbdf&f=dzep9n4
Also, they left this message for you: Hi Bruce,
Here is a zipped file of one of the subjects that I'm having label troubles with. The lh.v1.label isn't mapping correctly. I find the same goes for the aparc atlas as well (I haven't checked out anything else). If you could help me figure out why this is happening, that would be great!
Thanks, Krista
Please be aware, your upload will expire on December 31st. If you'd like to download these files, feel free to use the link below:
http://gate.nmr.mgh.harvard.**edu/filedrop2/?u=1079qbdfhttp://gate.nmr.mgh.harvard.edu/filedrop2/?u=1079qbdf
Cheers, The NMR Team
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/**compliancelinehttp://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.
Sorry, just one last thing. If the pial matter and white matter borders came out fine initially, is it necessary to rerun the whole recon-all automatic pipeline? I'm just asking because I have about 40 people that i will need to rerun because of this problem.
Thanks again! Krista
On Wed, Oct 9, 2013 at 8:47 PM, krista kelly krista.kelly16@gmail.comwrote:
Also, just to add to this, if I rerun recon in 5.1 starting from the normalization stage when I initially ran all subjects in 5.0, will this be a problem?
On Wed, Oct 9, 2013 at 8:05 PM, krista kelly krista.kelly16@gmail.comwrote:
Thanks Allison,
So to be clear, I just need to rename talairach.auto.xfm as talairach.xfm and then rerun recon-all from the normalization step? However, I'm not sure how to run recon starting from the normalization stage. Would you be able to help with that?
Also, I've been doing manual edits to the brain extraction as well as adding control points on all of my subjects and I'm wondering if this will negate any edits I've made. So I'm pretty much starting from scratch?
Thanks so much for looking into this for me!
Best, Krista
On Mon, Oct 7, 2013 at 12:19 PM, Allison Stevens < astevens@nmr.mgh.harvard.edu> wrote:
Hi Krista, I took a look at your subject and think I have determined the problem. Because your input data was high resolution (1.0000 x 0.9375 x 0.9375), the talairach registration step failed. If you look at the talairach.xfm, you'll see it is way off: tkregister2 --mgz --s BV20_2ndrun --fstal --surf orig
But the talairach.auto.xfm is correct. You can copy the talairach.auto.xfm to talairach.xfm and rerun from the -normalization step.
You might also want to look at these instructions: https://surfer.nmr.mgh.**harvard.edu/fswiki/HiResReconhttps://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon
They might not all apply to you but could potentially. Allison
---------- Forwarded message ----------
Date: Thu, 03 Oct 13 22:55:12 -0400 From: krista.kelly16@gmail.com To: fischl@nmr.mgh.harvard.edu Subject: V1 Labels
Hey!
Krista (krista.kelly16@gmail.com) has uploaded some files for you at the Martinos Center FileDrop:
-> BV20_2ndrun.zip (167.53 MiB) <http://gate.nmr.mgh.harvard.** edu/filedrop2/?u=1079qbdf&f=**dzep9n4http://gate.nmr.mgh.harvard.edu/filedrop2/?u=1079qbdf&f=dzep9n4
Also, they left this message for you: Hi Bruce,
Here is a zipped file of one of the subjects that I'm having label troubles with. The lh.v1.label isn't mapping correctly. I find the same goes for the aparc atlas as well (I haven't checked out anything else). If you could help me figure out why this is happening, that would be great!
Thanks, Krista
Please be aware, your upload will expire on December 31st. If you'd like to download these files, feel free to use the link below:
http://gate.nmr.mgh.harvard.**edu/filedrop2/?u=1079qbdfhttp://gate.nmr.mgh.harvard.edu/filedrop2/?u=1079qbdf
Cheers, The NMR Team
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/**compliancelinehttp://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
-
krista kelly