Another note, I just did a little experimenting, and it appears that using a RAS oriented image for the initial recon-all run (I've been using all LAS images) will fix the left-right flipping that occurs with mri_surf2surf.
However the mesh is still oriented incorrectly, such that a-p is facing superior-inferiror. -zack On Mon, Sep 29, 2014 at 1:07 PM, Zachary Greenberg < zacharyigreenb...@gmail.com> wrote: > Hi Doug, > > Thanks for your continued help with this. > > I use freeview -v rawavg.mgz -f lh.pial.native > > The problem I was mentioning in my first message though, is that the > native pial surface mesh output from mri_surf2surf is only oriented > correctly in freeview, but not in any other mesh viewer (such as Matlab, > Blender, Unity, Pyqt, etc...). > > For example, if I convert the lh.pial.native mesh to ascii with > mris_convert lh.pial.native lh.pial.native.asc, I can then use all the tri > and vert coordinates from that ascii file to plot the mesh in matlab (or > some other viewer by converting the .asc to .obj). > > Viewing the Mesh in any of those third party methods will reveal that the > mesh is flipped (left is right, so loading the left hem coords reveals the > right hem) and oriented such that the respective poles of the brain > (frontal and occipital) are pointing superior and inferior as apposed to > a-p. > > This is where I'm stumped. Does freeview do something to remap the > left-right flip and orient the mesh correctly? > > Thanks again. > > -zack > > On Wed, Sep 24, 2014 at 8:48 AM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> >> When I run your commands, the pial is correctly oriented and placed. >> What is your freeview command? This is what I use >> >> freeview -v rawavg.mgz --surface ../surf/lh.pial.native:edgecolor=yellow >> >> On 09/23/2014 06:11 PM, Zachary Greenberg wrote: >> > 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 >> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 >> > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> >> > Phone Number: 617-724-2358 <tel:617-724-2358> >> > Fax: 617-726-7422 <tel:617-726-7422> >> > >> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> > <http://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 <mailto: >> 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. >> > >> > >> > >> > >> > -- >> > *Zachary Greenberg* >> > /Assistant Imaging Specialist/ >> > /Department of Neurological Surgery/ >> > /University of California, San Francisco/ >> > >> > >> > >> > _______________________________________________ >> > 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 >> >
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