Hi Doug,
Thanks for getting back to me and sorry for the delay. Yes I can actually. If I corregister the CT to orig.nii and then pick out the points in freeview they look pretty good. This is a pretty painful process though. Is there an easy way to save a set of points in a text file from freeview?
Ideally, I would like to be able to do this with the native pial surface as well, but I still have the problem of it appearing rotated and flipped in freeview. Is there a way to fix this?
Thanks again for your help,
Best, -Zack
On Thu, Sep 18, 2014 at 12:50 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Can you get it to display correctly on the pial surface in conformed space?
On 09/17/2014 08:04 PM, Zachary Greenberg wrote:
Hello Freesurfer experts,
I am having a tough time getting my pial surfaces into the correct anatomical space. I work with ECoG Patients, so we have pre-implant high resolution T1s (GE SPGR), and post-implant high resolution CTs that show the location of ECoG electrodes within the patient's skull. Our goal: display ECoG electrodes in their correct positions on the patient's native pial surface.
Right now, my pipeline works like this: -ACPC align the T1, leave it in LAS orientation. -recon-all the acpc T1, using -3T -all -openmp 8 -use-gpu -corregister the CT to the acpc T1 (SPM), get electrode coords in T1
space
-plot the electrodes on the resultant .pial surface from freesurfer
The problem is, I can definitely tell that the position of the pial mesh is off (probably by 10 millimeters or so), as the electrodes (which have the correct coordinates from the T1 correg, confirmed visually by overlaying the CT on T1) are not in their correct positions on the mesh. Likewise, DTI fibers reconstructed from EPIs correctly corregistered to the T1 also appear off position within the .pial mesh.
Here is what I have tried:
compute the transform from .pial to .pial.native as suggested on https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
tkregister2 --mov rawavg.mgz --targ orig.mgz --reg register.native.dat
--noedit --regheader
mri_surf2surf --sval-xyz pial --reg register.native.dat rawavg.mgz
--tval lh.pial.native --tval-xyz --hemi lh --s subjectname
This results in a mesh that is flipped (left is right) and rotated such that anterior is inferior (frontal cortex is pointing downward). The mesh appears this way when plotted in any viewer besides freesurfer (MATLAB mesh, Pyqt) but appears in the correct orientation in freeview. Replacing orig.mgz with the original T1.nii in the command above produces the opposite effect, freeview plots the orientation wrong, and any other viewer plots the Mesh oriented correctly, and the mesh appears to be identical to the originally output .pial mesh (electrodes are still wrong).
Any help in pin pointing what is going wrong here would be greatly appreciated. I have a feeling it has something to do with the mesh being in surface RAS and the original T1 being in LAS.
Thanks a bunch, -Zack
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.