Pipefix

ok guys, I’ve put in some changes to flirt>img2stdcoord.cc

I think that many users don’t even know that it can be used “interactively” (I know this is a strong assumption). I think its better to just remove “interactive mode” altogether. It’s not really the kind of program that provides any incentive, or added utility by being interactive.

I’ve made the changes, but obviously want some input to see if you guys think this is too much of a breakage to the code.

3 ways to run it now:

One

img2stdcoord -img /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz -std /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz -vox coordinates.txt

12 -48 -42 20 -38 -46 18 -44 -46 24 -36 -44 24 -36 -44 22 -42 -44

Two

cat coordinates.txt | img2stdcoord -img /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz -std /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz -vox

12 -48 -42 20 -38 -46 18 -44 -46 24 -36 -44 24 -36 -44 22 -42 -44

Three

img2stdcoord -img /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz -std /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz -vox

Interactive mode has been removed. Please pipe input such as: cat coordinate_file.txt | img2stdcoord, OR supply a coordinate file