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
Undoubtedly, your 001.mgz has larger voxels, and so there will be some changes in seg volumes. A better way to do this is with mri_label2vol. First, you'll need the right registration file. Get that with:
tkregister2 --mov 001.mgz --targ orig.mgz --regheader --reg reg.001.dat --noedit
Now run mri_label2vol:
mri_label2vol --reg reg.001.dat --seg aseg.mgz --temp 001.mgz --o aseg-in-001.nii
You will still have changes in volumes, but I think this is the best you can do
doug
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
Jared,
Try adding the flag -ns 1 to your mri_convert command.
Nick
On Wed, 2009-02-18 at 11:33 -0500, 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
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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
and how do you measure volume? Certainly the voxel count is bound to change since your voxel size is changing. The volume will certainly change as well.
cheers, Bruce On Thu, 19 Feb 2009, Jeff Dewey wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
Jared Price -
Jeff Dewey -
Nick Schmansky