Hi Tamara
we don't use an intensity threshold as such. If you are looking for CSF,
why not use our aseg and erode it once to avoid border voxels? Or twice if
you want to be really certain.
I'll leave (2) for one of our longitudinal processing experts.
cheers
Bruce
On Thu, 26 Jan 2017, Tamara Tavares wrote:
Hello,
I have two questions which I was hoping to get some help with.
(1) I was wondering whether there was a intensity threshold for grey matter
and CSF. I know that Freesurfer scales the intensity so white matter has an
intensity of 110 (as can be seen at the bottom of Freeviewer when I open the
brianmask.mgz). I was wondering whether there is a threshold value I can use
to indicate whether a voxel is part of the CSF with 100% confidence?
(2) After I make edits to my aseg output in the longitudinal stream, do I
just run the following command to recreate the final volumes:
recon-long -autorecon2-noaseg -subjid <Subj_ID>
I assume the -subjid is the name of the edited time point and <Subj_ID>
is the name of the recreated volumes?
Thank you,
Tamara
_______________________________________________
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.
