Hello freesurfers,
I am currently trying to create a normalized .mgz file using the
mri_ca_normalize command. Instead of using a .gca atlas, I am using a
manually segmented image.
I have tried using the -seg flag. However, I keep getting an error that
I am not inputting the correct arguments. Do you have to include the .gca
and transform file in the command, even if they will not be used? The
fswiki section on GCA atlases does not seem to touch on this.
For instance, which of the following would be the correct command line?
1.) mri_ca_normalize -seg <seg_file> <input volume> <output_file>
or
2.) mri_ca_normalize -seg <seg_file> <input volume> <GCA atlas> <transform
file> <output_file>
Thanks for the help!
~ Mark
_______________________________________________
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.
