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I'm using Slicer as part of a pipeline for ADC quantification. I convert T1 and T2 files from dicom 2 nifti using dcm2niix and DWI dicom to nifti using DWIConvert. ADC is easily computed using a R script. ROI are drawn on the registered T1w and T2w images using Slicer editor (T1w as master volume).
All the series were acquired using the same orientation (purely axial) but qform matrix differ if I use DWIConvert or dcm2niix or mcverter in order to transform them from DICOM to NIFTI. Quite strange but this is the situation so I need to solve this issue.
I use a R script to obtain the statistics so I need to move the ROI from its T1w's ijk space to the ijk space of the ADC nifti. I use (qform_ADC)^-1 * qform_ROI to transform the ijk indexes of those positions labeled in the ROI .
It looks quite easy but labelled regions do not move to the place where they are supposed to move to. i.e. I label a slice of one ventricle and I look where this region is moved on the ADC, it does not match with that region on the ADC after this operation.
Is (qform_ADC)^-1 * qform_ROI the correct operation? (* means matrix multiplication, ^-1 means matrix inversion)