search

pyushkevich / greedy

Very fast greedy diffeomorphic registration code
GNU General Public License v3.0
59 stars 16 forks source link

Weird demofrmation following Quick Start guide #7

Closed vzickus closed 5 years ago

vzickus commented 5 years ago

Following the quick start guide here and using -d 2 instead of -d 3, using the images provided in the /matlab/diff directory, I get a weird deformation. Below shows (fixed, moving, warped) images from top to bottom. I also include the deformation field. Any ideas why this is the case?

brain_fixed brain_moving resliced warp.nii.gz

pyushkevich commented 5 years ago

Hello,

I cannot reproduce this error. Here are the commands I ran and reasonable-looking output that I get. Please check that you are using the current code.

#!/bin/bash greedy -d 2 -a -m NCC 2x2x2 -i brain_fixed.png brain_moving.png -o affine.mat -ia-image-centers -n 100x50x10

greedy -d 2 -m NCC 2x2 -i brain_fixed.png brain_moving.png -it affine.mat -o warp.nii.gz -n 100x50x10 -n 100x50x10

greedy -d 2 -rf brain_fixed.png -rm brain_moving.png reslice_brain_moving.png -r warp.nii.gz affine.mat

image

Paul

vzickus commented 5 years ago

Ah, OK, I did not use "-n 100x50x10" twice like you show here. It works now.

Curiously, I tried reproducing the error with commands I used initially (just looking up the history in the terminal) and could not do it. Oh well!