Hi Nicholas,In such situations, I have learned that autorecon2-wm after adding WM voxels seems to work pretty well. Hope that helps.Best Wishes,ElijahOn 27 September 2017 at 16:46:43, Nicholas Goh (ngoh95@gmail.com) wrote:
Bruce,Thank you for the response. Attempting to use this method has not produced results, and I am unsure how to proceed or if I had performed it improperly. I have attached an example of the control points being placed, if that helps any.Thank you,Nicholas Goh______________________________
On Wed, Sep 27, 2017 at 11:04 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Nicholas
yes, possibly, depending on why you are missing chunks. If the white matter in the regions you are missing has intensity values significantly < 110 then what you are doing should help. The control.dat file must be place in the subject/tmp dir for us to find it.
cheers
Bruce
On Wed, 27 Sep 2017, Nicholas Goh wrote:
I am attempting to fix the aparc+aseg.mgz file for an image, and wanted to check to see if I am
doing it correctly.What I was doing which seemed to be ineffective was
1)create a new point set of control points labelled control.dat
2)place control points along what should be white matter
3)save point set
4)run recon-all -autorecon2-cp -autorecon3 -subjid XXXX
Is this the correct way to go about fixing aparc+aseg files that are missing chunks of the brain? Is
there a better way to go about this?
Thanks for the help,
Nicholas Goh
_______________________________________________
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 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.