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.
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
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