the way you have it set up, it is sampling on the gray/white boundary ("white" surface). You can sample midway into the ribbon with --projfrac 0.5 doug
Omer Tal wrote:
Hey Doug,
Attached is a picture showing the resulting surface file. Note that the red regions correspond to the number 2 (white matter) and the yellow regions correspond to numbers between 1000 and 1035 (gray matter). If the conversion would be completed correctly, only numbers between the 1000 and 1035 should come up on the surface.
Thank you for your time and help, Omer Tal
can you post a picture?
Omer Tal wrote:
Hey Doug,
Tried, no change unfortunately.
Here is the output, just in the case: mri_vol2surf --src aparc+aseg.nii --surf orig --ref orig.mgz --regheader 111123 --hemi lh --o test.mgh srcvol = aparc+aseg.nii srcreg unspecified srcregold = 0 srcwarp unspecified surf = orig hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /home/otal/raweegmeg/structuralDB//111123/mri/orig.mgz as target reference. Reading surface /home/otal/raweegmeg/structuralDB//111123/surf/lh.orig Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 100537 Writing to test.mgh Dim: 157373 1 1
Thank you, Omer Tal
Hi Omer, Try removing "--srcreg identity" doug
Omer Tal wrote:
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve