To answer your question more completely, we're trying to compare two files with the following headers:
Freesurfer segmentation: height = 256 width = 256 depth = 256 nframe = 1 imnr0 = 1 imnr1 = 256 xnum = 256 ynum = 256 fov = 256.000000 thick = 1.000000 xstart = -128.000000 xend = 128.000000 ystart = -128.000000 yend = 128.000000 zstart = -128.000000 zend = 128.000000 type = 0 xsize = 1.000000 ysize = 1.000000 zsize = 1.000000 x ras = -1.000000 0.000000 0.000000 y ras = 0.000000 0.000000 -1.000000 z ras = 0.000000 1.000000 0.000000 c ras = 0.000000 -0.000015 17.750004 det(xyz_ras) = -1.000000 ras_good_flag = 1 brightness = 1 subject_name = path_to_t1 = fname_format =
Target image: height = 256 width = 256 depth = 120 nframe = 1 imnr0 = 1 imnr1 = 120 xnum = 256 ynum = 256 fov = 256.000000 thick = 1.000000 xstart = -128.000000 xend = 128.000000 ystart = -128.000000 yend = 128.000000 zstart = -60.000000 zend = 60.000000 type = 3 xsize = 0.976562 ysize = 0.976562 zsize = 1.300000 x ras = 1.000000 0.000000 0.000000 y ras = 0.000000 -1.000000 0.000000 z ras = 0.000000 0.000000 1.000000 c ras = 0.000000 0.000000 17.749996 det(xyz_ras) = -1.000000 ras_good_flag = 1 brightness = 1 subject_name = path_to_t1 = fname_format =
It's also acceptable to convert the target image to the freesurfer output space, as long as structure volumes in the segmentation are preserved.
Thanks again, Jeff
Bruce Fischl wrote:
what are the voxel sizes?
On Wed, 18 Feb 2009, Jared Price wrote:
Dear gurus, when running mri_convert -rt nearest -ot nii -rl 001.mgz seg_edited.mgz seg_edited_axial.nii to reslice from coronal to axial space we are seeing some significant volume changes in the segmentation. Anyone know why or how to fix it. Jared _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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