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 gr...@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.
