External Email - Use Caution
I extract the streamlines for each tract from path.pd.trk to an ascii file and then wish to transform the coordinates to RAS T1 coordinates in millimeters. My results are not correct.
Here is the extraction command I'm using. Is this correct? Perhaps I should be using orig.mgz as the outref volume? I do not understand -inref and --outref dmri_trk2trk -in path.pd.trk -inref path.pd.nii.gz -outref path.pd.nii.gz -outasc test.streamlines
Given the above command, I am assuming that the output I'm getting is in the diffusion frame in voxel coordinates. I extract 4x4 transforms and apply them in sequence; I append 1.0 to each 3-vector before applying them of course. Here is the most compact approach I've tried 1st transform: mri_info -in path.pd.nii.gz -vox2ras-tkr 2nd transform: mri_info -in orig.mgz -tkr2scanner
I've also tried this: 1st transform: mri_info -in path.pd.nii.gz -vox2ras 2nd transform: mri_info -in path.pd.nii.gz -scanner2tkr 3rd transform: mri_inf -in orig.mgz -tkr2scanner
I've tried some other sequence since I'm not sure what frame is the target output for the-vox2ras* transforms stored in path.pd.nii.gz . Those are the only transforms which contain the multiplication factors needed to get to millimeters from voxels.
Rather than continuing to fumble around, some direction from you who know would be very much appreciated.
Best - Don