Hello,
I apologize for asking such a basic question, but I can’t find the right tool to interpolate a NIFTI brain volume (or DICOMs) into the raster coordinates of a second volume. I simply want a naive interpolation into the second volume’s coordinate system without performing registration. For my application I do not want to actually register the two volumes, just interpolate/resample.
I tried using mrivol2vol.m in Matlab but it crashes because it can’t find the field ‘mov.vox2ras0’ in my NIFTI headers (I use either mri_convert or dicm2nii to convert Siemens DICOMs to NIFTI).
I then tried manually calculating the raster coordinates for the two volumes by creating integer voxel coordinates for (i,j,k) and then multiplying them by the NIFTI vox2ras matrix to get (x,y,z). I then use ‘scatteredInterpolant’ in Matlab to interpolate one volume into the second volume’s coordinate system, but this has only worked for me some of the time. I have been able to interpolate 2D axial MRI slices into an oblique 2D coordinate system, but I’m having trouble with 3D acquisitions like MPRAGE, etc.
Does anyone know of a “foolproof” and simple standalone tool for this task (ideally for Matlab)?
--- Jason
-- Jason Stockmann Instructor in Radiology Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown, MA 02129 jstockmann@mgh.harvard.edumailto:jstockmann@mgh.harvard.edu +1 315 450 3309
Hi Jason
you can use -rl ("reslice like"):
mri_convert -rl vol2.mgz vol1.mgz vol1_like_vol2.mgz
cheers Bruce
On Sun, 3 Mar 2019, Stockmann, Jason wrote:
Hello,
I apologize for asking such a basic question, but I can’t find the right tool to interpolate a NIFTI brain volume (or DICOMs) into the raster coordinates of a second volume. I simply want a naive interpolation into the second volume’s coordinate system without performing registration. For my application I do not want to actually register the two volumes, just interpolate/resample.
I tried using mrivol2vol.m in Matlab but it crashes because it can’t find the field ‘mov.vox2ras0’ in my NIFTI headers (I use either mri_convert or dicm2nii to convert Siemens DICOMs to NIFTI).
I then tried manually calculating the raster coordinates for the two volumes by creating integer voxel coordinates for (i,j,k) and then multiplying them by the NIFTI vox2ras matrix to get (x,y,z). I then use ‘scatteredInterpolant’ in Matlab to interpolate one volume into the second volume’s coordinate system, but this has only worked for me some of the time. I have been able to interpolate 2D axial MRI slices into an oblique 2D coordinate system, but I’m having trouble with 3D acquisitions like MPRAGE, etc.
Does anyone know of a “foolproof” and simple standalone tool for this task (ideally for Matlab)?
--- Jason
--
Jason Stockmann
Instructor in Radiology
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Charlestown, MA 02129
jstockmann@mgh.harvard.edu
+1 315 450 3309
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Stockmann, Jason