Hi John
when you say that they are oriented correctly in freeview, does that mean
that they just overlay properly on the volume? Or that e.g. what freeview
thinks is anterior is actually anterior, etc...?
cheers
Bruce
On Mon, 29 Feb 2016, John
Plass wrote:
Hello Freesurfer Experts,
I wrote in recently about my parcellation troubles with an ex-vivo scan
(link). Digging further, I've found that the surfaces I've produced
following the Ex-Vivo recon instructions are oriented properly when viewed
in freeview (freeview -v mri/orig.mgz -f surf/rh.white:edgecolor=blue
surf/rh.pial:edgecolor=red), but are misoriented in tkmedit (tkmedit $SUBID
orig.mgz rh.white). I suspect that something related this might be the
source of the parcellation problems. Any idea why this might be and how I
can fix it?
Relevant background information:
*volumes were reoriented before FS processing using the command "mri_convert
-c -iid 0 -1 0 -ijd 0 0 -1 -ikd 1 0 0 mprage.nii.gz mprage.mgz"
*running freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 on Ubuntu 14.04
As always, I'm very grateful for any help you can provide.
John
_______________________________________________
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.
