Hello Freesurfer experts,
I have two separate questions.
1. I am doing an MRI study on young children (3-5 years old). I have read in a few a different places that Freesurfer isn't ideal for analyzing young subjects. It does seem to be processing my subjects just fine though, with the exception of needing a bit of editing on a few images. Out of curiosity, I would like to try using a different template to register my subjects to. I know Freesurfer uses an MNI based adult template, and I have acquired a template for my specific age group. Is it possible for me to replace the Freesurfer template with my own. How would I go about doing this, and do you expect the results I get to be better or worse than using the adult template.
2. When I do white matter edits, they seem to be getting overwritten when I rerun the subject. I am editing the wm.mgz volume, making sure that I save it, and then rerunning the following line
recon-all -s subject -autorecon2 -autorecon3
I've also tried running from different places in the pipeline (-autorecon2-cp, -autorecon2-wm) and it still does not work. Any idea whats going wrong here, and how I might fix this.
Greatly appreciate any help with this
Matt
Hi Matt
1. What template do you mean? We have multiple ones. The only MNI one we have is for the linear talairach registration, which we barely use at all.
2. How are you doing the editing? Is it in freeview or tkmedit? When we edit the wm.mgz we track it by setting erased voxels to 1 (not 0) and draw-in ones to 255. Is that happening in your edited wm.mgz volumes?
cheers Bruce
On Fri, 13 Jun 2014, Walton, Matt wrote:
Hello Freesurfer experts, I have two separate questions.
- I am doing an MRI study on young children (3-5 years old). I have read in
a few a different places that Freesurfer isn't ideal for analyzing young subjects. It does seem to be processing my subjects just fine though, with the exception of needing a bit of editing on a few images. Out of curiosity, I would like to try using a different template to register my subjects to. I know Freesurfer uses an MNI based adult template, and I have acquired a template for my specific age group. Is it possible for me to replace the Freesurfer template with my own. How would I go about doing this, and do you expect the results I get to be better or worse than using the adult template.
- When I do white matter edits, they seem to be getting overwritten when I
rerun the subject. I am editing the wm.mgz volume, making sure that I save it, and then rerunning the following line
recon-all -s subject -autorecon2 -autorecon3
I've also tried running from different places in the pipeline (-autorecon2-cp, -autorecon2-wm) and it still does not work. Any idea whats going wrong here, and how I might fix this.
Greatly appreciate any help with this
Matt
Hey Bruce,
I'm referring to the MNI305 which freesurfer uses for linear registration. I know this is an adult template, and I wanted to try and use an NIH atlas designed from 2-5 year olds (same age as my subjects). I was interested in seeing if I get different results from the MNI305.
As for the WM edits, I am doing this in Freeview. Using voxel edit, Freehand, eraser value set to 255, brush value set to 0. I imagine this is incorrect from your previous response.
Thanks for your help, most appreciated
Matthew Walton ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: June-13-14 3:34 PM To: Freesurfer support list Subject: Re: [Freesurfer] template registration and wm edits
Hi Matt
1. What template do you mean? We have multiple ones. The only MNI one we have is for the linear talairach registration, which we barely use at all.
2. How are you doing the editing? Is it in freeview or tkmedit? When we edit the wm.mgz we track it by setting erased voxels to 1 (not 0) and draw-in ones to 255. Is that happening in your edited wm.mgz volumes?
cheers Bruce
On Fri, 13 Jun 2014, Walton, Matt wrote:
Hello Freesurfer experts, I have two separate questions.
- I am doing an MRI study on young children (3-5 years old). I have read in
a few a different places that Freesurfer isn't ideal for analyzing young subjects. It does seem to be processing my subjects just fine though, with the exception of needing a bit of editing on a few images. Out of curiosity, I would like to try using a different template to register my subjects to. I know Freesurfer uses an MNI based adult template, and I have acquired a template for my specific age group. Is it possible for me to replace the Freesurfer template with my own. How would I go about doing this, and do you expect the results I get to be better or worse than using the adult template.
- When I do white matter edits, they seem to be getting overwritten when I
rerun the subject. I am editing the wm.mgz volume, making sure that I save it, and then rerunning the following line
recon-all -s subject -autorecon2 -autorecon3
I've also tried running from different places in the pipeline (-autorecon2-cp, -autorecon2-wm) and it still does not work. Any idea whats going wrong here, and how I might fix this.
Greatly appreciate any help with this
Matt
Hi Matt
yes, you need to set them to 1 I believe, not 0. The most recent version of freeview has a "recon edit" mode, which will do this automatically.
As far as using your own template, that should be pretty straightforward. Hopefully either Nick or Avi can let you know how
cheers Bruce On Mon, 16 Jun 2014, Walton, Matt wrote:
Hey Bruce,
I'm referring to the MNI305 which freesurfer uses for linear registration. I know this is an adult template, and I wanted to try and use an NIH atlas designed from 2-5 year olds (same age as my subjects). I was interested in seeing if I get different results from the MNI305.
As for the WM edits, I am doing this in Freeview. Using voxel edit, Freehand, eraser value set to 255, brush value set to 0. I imagine this is incorrect from your previous response.
Thanks for your help, most appreciated
Matthew Walton ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: June-13-14 3:34 PM To: Freesurfer support list Subject: Re: [Freesurfer] template registration and wm edits
Hi Matt
- What template do you mean? We have multiple ones. The only MNI one we
have is for the linear talairach registration, which we barely use at all.
- How are you doing the editing? Is it in freeview or tkmedit? When we
edit the wm.mgz we track it by setting erased voxels to 1 (not 0) and draw-in ones to 255. Is that happening in your edited wm.mgz volumes?
cheers Bruce
On Fri, 13 Jun 2014, Walton, Matt wrote:
Hello Freesurfer experts, I have two separate questions.
- I am doing an MRI study on young children (3-5 years old). I have read in
a few a different places that Freesurfer isn't ideal for analyzing young subjects. It does seem to be processing my subjects just fine though, with the exception of needing a bit of editing on a few images. Out of curiosity, I would like to try using a different template to register my subjects to. I know Freesurfer uses an MNI based adult template, and I have acquired a template for my specific age group. Is it possible for me to replace the Freesurfer template with my own. How would I go about doing this, and do you expect the results I get to be better or worse than using the adult template.
- When I do white matter edits, they seem to be getting overwritten when I
rerun the subject. I am editing the wm.mgz volume, making sure that I save it, and then rerunning the following line
recon-all -s subject -autorecon2 -autorecon3
I've also tried running from different places in the pipeline (-autorecon2-cp, -autorecon2-wm) and it still does not work. Any idea whats going wrong here, and how I might fix this.
Greatly appreciate any help with this
Matt
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Walton, Matt