From af9d3a3d0658547c1bd9de64396bb6bd85359221 Mon Sep 17 00:00:00 2001
From: Anna <17569461+zapaishchykova@users.noreply.github.com>
Date: Thu, 10 Aug 2023 10:49:54 -0400
Subject: [PATCH] bash mappings.csv

---
 .Rhistory                    |  0
 README.md                    | 15 +--------------
 example_dataset/mappings.csv |  4 ----
 3 files changed, 1 insertion(+), 18 deletions(-)
 create mode 100644 .Rhistory
 delete mode 100644 example_dataset/mappings.csv

diff --git a/.Rhistory b/.Rhistory
new file mode 100644
index 0000000..e69de29
diff --git a/README.md b/README.md
index ac39fcd..3962a9f 100644
--- a/README.md
+++ b/README.md
@@ -48,20 +48,7 @@ The `annotation.csv` has a following structure (with no header):
 
 ## Tutorial
 
-1. **Prepare the dataset:** 
-
-    - **Option 1 - Provide a mappings.csv file**
-
-      Create a `mappings.csv` file in the inputs folder specifying the `img_path` and the respective `mask_path`. Se bellow an example of the content of this file:
-        ```
-        img_path,mask_path
-        data/1.nrrd,/path/to/respective/1_mask.nii.gz
-        data/2.nii.gz,/path/to/respective/2_mask.nii.gz
-        ...
-        ```
-      > :warning: The name of the file must be `mappings.csv` and the first line must contain the column names `img_path` and `mask_path`.
-
-    - **Option 2 - Structure the input data folder (only works for nifti)**
+1. **Prepare the dataset:Structure the input data folder (only works for nifti)**
 
       To get started, create a folder with the following file structure:
 
diff --git a/example_dataset/mappings.csv b/example_dataset/mappings.csv
deleted file mode 100644
index 2d2038a..0000000
--- a/example_dataset/mappings.csv
+++ /dev/null
@@ -1,4 +0,0 @@
-img_path,mask_path
-example_dataset/sub-pixar007_T1w.nii.gz,example_dataset/sub-pixar007_T1w_mask.nii.gz
-example_dataset/sub-pixar008_T1w.nii.gz,example_dataset/sub-pixar008_T1w_mask.nii.gz
-example_dataset/sub-pixar009_T1w.nii.gz,example_dataset/sub-pixar009_T1w_mask.nii.gz
\ No newline at end of file