Registration DTI and DW-MRS data

[chloé najac]

Hi,

We acquired DTI data using 3T Philips MRI scanner (data exported in PAR/REC). In addition, we are also collecting DW-MRS data from the same volunteers. We would like to extract DTI data from the volume-of-interest (VOI) of the MRS acquisition. To do so, we are currently using the following steps:

1/ we are converting our DTI PAR/REC data into nifti files in ExploreDTI and process our DTI data to create FA/MD/etc. maps in ExploreDTI. At that point the maps are in .mat format.

2/ we are exporting the FA/MD/… maps as nifti files (this is also done in ExploreDTI)

3/ we have a separate pipeline (Matlab-based) to extract the FA/MD/… data from our MRS VOI (this code works with nifti format)

However, we seem to have an issue with the coordinates of the nifti images created in ExploreDTI.

When overlaying the FA map with the native T1w images in FSL, we seem to have a shift in the anterior-superior direction, so that the FA maps seems shifted down by approximately half the size of the stack. We can then see that if we mask the FA map with our VOI (step 3), it does not properly overlap with the brain (while it does with the T1w images).

Is it possible that the nifti images post ExploreDTI are not in the same space as the native ones from the scanner? Is there a way to bring them to their original coordinates so that they overlay with the T1w images outside of ExploreDTI?

Many thanks for the help,

Chloe