Open rwickens opened 1 month ago
https://github.com/vfonov/RMINC/blob/597b17a9bd319f8b3c15ff2718fab1ca84e6e9e9/R/minc_vis2D.R#L642 - it should work with RMINC_flip_image
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?
check direction_cosines property of spatial coordinates, perhaps your image is stored with flipping coordinate transform. (i.e mincheader <filename>.mnc|grep direction_cosines
)
Thanks, flipping the image using mincresample instead of c3d solved the problem.
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