As an update, I’ve tried using two other dcm-to-nii converters: MRIconvert (MRIConvert files — LCNI) and Mango (Research Imaging Institute — Mango).
With MRIconvert I seem to run into the same problem as before with Xiangrui Li’s converter (image 1).
With Mango, it seems to have shifted all coordinates (image 2).
I have also tried just flipping the image and saving it again (image 3). Seems to work but alignment is still a bit out.
CoregSeg_ConversionExamples.pdf (113.5 KB)
Essentially the voxel placements were aligned to the posterior gray matter and parietal white matter as indicated in:
Lin, A., Tran, T., Bluml, S., Merugumala, S., Liao, H. J., & Ross, B. D. (2012, September). Guidelines for acquiring and reporting clinical neurospectroscopy. In Seminars in neurology (Vol. 32, No. 04, pp. 432-453). Thieme Medical Publishers. DOI: 10.1055/s-0032-1331814
Would I need to specify the folder containing all of the associated dicom files? I have tried that but keep getting the error:
Error using spm_vol>spm_vol_hdr (line 80)
File “H:\PhD\RA-MRS\Jobfiles\ErrorChecks\sub-43\ses-01\anat” does not exist.