how are you doing the nonlinear registration? And why not using a rigid transform? It is the same subject, isn't it? Are you correcting for eddy currents?
On Thu, 1 Apr 2010, Walimuni, Indika S wrote:
Yes, After non-linear registration to DTI space then overlay. Truly, Indika Walimuni Research Associate University of Texas Health Science Center Houston, TX. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, April 01, 2010 2:06 PM To: Walimuni, Indika S Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Volume masks
that shouldn't create much blurring. How are you assessing this? By overlaying on the DTI volume? If so, how did you register it?
On Thu, 1 Apr 2010, Walimuni, Indika S wrote:
Hi Bruce Sure, Its 170x256x256 axial Truly, Indika Walimuni Research Associate University of Texas Health Science Center Houston, TX. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, April 01, 2010 1:45 PM To: Walimuni, Indika S Subject: RE: [Freesurfer] Volume masks
Hi Indika,
can you post these to the list so others can answer? What is the "native" space you are using?
Bruce
On Thu, 1 Apr 2010, Walimuni, Indika S wrote:
Hi Bruce Thanks for the reply. I used wmparc.mgz file for all the
cortical and sub-cortical WM/GM masks. This was the command, mri_binarize --i wmparc.mgz --match "index from LUT" --o outputfile. This effect becomes even more significant after I register the mask to like DTI/FA. But I don't think it is a FreeSufer issue. I think I may have judged based on that. The masks seems fine in the FreeSurfer space and the masks are OK. But when I convert them to our native space using "mri_convert" I see a broadening around the edges. I just want to test if there is another way and see the difference. Am I using the wrong file? If I am to use aparc+aseg.mgz file can I use it for all cortical, subcortical, WM and GM masks?
Truly, Indika Walimuni Research Associate University of Texas Health Science Center Houston, TX. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, April 01, 2010 11:38 AM To: Walimuni, Indika S Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume masks
Hi Indika,
you should be able to do this using the aparc+aseg.mgz volume and mri_binarize. What command line did you use and can you give us an example of the "spilling"?
cheers, Bruce
On Thu, 1 Apr 2010, Walimuni, Indika S wrote:
Hi FreeSurfer List Is their any way that I can generate cortical
and sub-cortical volume masks by using the surfaces generated by FreeSurfer. If I can could anyone give me the proper command. Apparently, The masks I already generated using mri_binarize command, are little bigger and spilling into the surrounding.
Thank you in advance, Truly, Indika Walimuni Research Associate University of Texas Health Science Center Houston, TX. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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