From 913e6c2dd1a1ddff762e49dffb1daa1ec241c133 Mon Sep 17 00:00:00 2001 From: JoshuaHess12 Date: Tue, 20 Apr 2021 14:58:47 -0400 Subject: [PATCH] update readme --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 0907bbf..781f5f0 100644 --- a/README.md +++ b/README.md @@ -29,7 +29,7 @@ If you are unable to use Docker on your machine, then you can still use hdi-reg: Options for importing data and processing are listed below. Detailed descriptions of each function can be found within source code. | hdi-reg Step | Options | | --- | --- | -| 1.`command_elastix.py` | image registration between fixed image and moving image | +| 1. `command_elastix.py` | image registration between fixed image and moving image | | `--fixed` | path to fixed image (Ex. `--fixed ./fixedImage.nii`) | | `--moving` | path to moving image (Ex. `--moving ./movingImage.nii`) | | `--out_dir` | path to output directory (Ex. `--out_dir ./outdirectory`) | @@ -37,7 +37,7 @@ Options for importing data and processing are listed below. Detailed description | `--mp` | path to manual landmark points (Ex. `--mp ./movingPoints.txt`) | | `--fp` | path to manual landmark points (Ex. `--fp ./fixedPoints.txt`) | | `--fMask` | fixed image mask to draw samples from during optimization (Ex. `--fMask ./fixedMask.nii`) | -| 1.`command_transformix.py` | transform images using saved transformation from elastix | +| 2. `command_transformix.py` | transform images using saved transformation from elastix | | `--in_im` |path to image to transform (can be multichannel) (Ex. `--in_im ./movingMultichannel.nii`) | | `--out_dir` | path to output directory (Ex. `--out_dir ./outdirectory`) | | `--tps` | path(s) to parameter files exported from elastix (Ex. `--tps ./affineTransformParameters.txt --tps ./nonlinearTransformParameters.txt`) |