From rwickens at protonmail.com  Fri Jul 19 17:37:41 2024
From: rwickens at protonmail.com (RW)
Date: Fri, 19 Jul 2024 21:37:41 +0000
Subject: [MINC-users] mincPlotSliceSeries - anatomical vs. radiological
 perspective
Message-ID: <cv8QL3FLobLH1r8qCIrphnoo-r-TFSsoCrUu9Mn4yNY2uV7DrmuTpflrTV7VZIcpxhKQHEBxr2N_8PaKtL86Tny-49VdlZUNxwi0Fn8cN-4=@protonmail.com>

Hi minc users,

I'm looking for support on the RMINC function "mincPlotSliceSeries", which appears to show images in radiological rather than anatomical perspective, which I would like to switch.

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](https://rawgit.com/Mouse-Imaging-Centre/RMINC/master/inst/documentation/visualizationTutorial.html)
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

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](https://github.com/joshunrau/majestic-minc)

Any help greatly appreciated,

RW