mincPlotSliceSeries appears to display images in radiological perspective

[rwickens]

Hello,

RMINC function mincPlotSliceSeries appears to show images in radiological rather than anatomical perspective.

Surprisingly, my attempts to resolve this by mirror-imaging the brain images beforehand have led to identical results.

How I'm calling the function:

library(RMINC) options(RMINC_flip_image=TRUE) #suggested by Jason Lerch for mac computers; otherwise upside down; see link anatVol <- mincGetVolume("/Users/rwick/Desktop/anat_vol.mnc") stat_path <-mincGetVolume("/Users/rwick/Desktop/stat_vol.mnc") mincPlotSliceSeries(mincArray(anatVol), # the anatomical volume mincArray(stat_path),
anatLow=0, anatHigh=500, # set anatomy thresholds low=0, high=3.5, # set stats thresholds symmetric=F,
begin=20, end=100, legend="t-statistics", dimension = 2)

Command for mirror-imaging the brains beforehand: c3d input_file_path -flip x -o mirrored_file_path

Relevant brain images attached:
neuroImages.zip

I'm using RMINC version 1.5.3.0. on R version 4.1.3 (2022-03-10) on conda (fork of minc-toolkit including native builds for Apple ARM64 architecture link

[vfonov]

https://github.com/vfonov/RMINC/blob/597b17a9bd319f8b3c15ff2718fab1ca84e6e9e9/R/minc_vis2D.R#L642 - it should work with RMINC_flip_image

[rwickens]

Hi @vfonov, I'm already setting RMINC_flip_image=TRUE because otherwise it's upside-down (Jason Lerch seems to suggest that this happens on macs). Any work-arounds?

[vfonov]

check direction_cosines property of spatial coordinates, perhaps your image is stored with flipping coordinate transform. (i.e mincheader <filename>.mnc|grep direction_cosines)

[rwickens]

Thanks, flipping the image using mincresample instead of c3d solved the problem.