Hey Doug, Test.nii is a volume nii (1x1x1mm) with values of interest per voxel, created using the header from brain_T1.nii which was simply created by using mri_convert from the subject's original brain.mgz. The *.nii file loads fine and matches the subject as expected. It is when trying to go back to surface, that things seem to get messy.
Thank you very much for your time, Omer Tal Keck Center for Functional MRI, UCSD > What is test.nii? How was it derived? > > Omer Tal wrote: >> Hey all, >> >> I am running into a bit of a problem converting back from a volume into >> a >> surface and was hoping someone would have some insight. >> >> I have an .nii volume for a given subject, and I want to convert it into >> a >> surface mgh file, so i can view it on tksurfer. Since its the same exact >> subject, I figured it should be relatively easy, but in the resulting >> surface all the white matter and gray matter voxels are mixed together >> (looks like tiger pattern on tksurfer) in the entire brain. I would >> point >> out though that the gray matter voxels do show up in the correct >> location >> (i.e. a motor gray voxel in my volume still ends up in the motor cortex >> in >> the mgh file), its just that they are surrounded with vertices which >> have >> white matter values. >> >> Any advice? >> >> Code: mri_vol2surf --src test nii --srcreg identity --ref T1.mgz >> --regheader test_subj --hemi lh --o test.mgh >> >> Thank you very much for your help, >> Omer Tal >> Keck Center for Functional MRI, UCSD >> >> _______________________________________________ >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > 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. > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
