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
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Jason Stockmann
Instructor in Radiology
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Charlestown, MA 02129
+1 315 450 3309