Merge pull request #7 from HealthBioscienceIDEAS/4-add-quick-dcm2niix…

…-intro

Stray commit that wasn't done before

episodes/imaging-data-structure-and-formats.Rmd

@@ -44,7 +44,7 @@ example [dcm2niix](https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPag
 
 :::::::::::::::::::::: discussion
 If you are interested in trying out converting DICOM data to Nifti, we have some 
-sample DICOM data for you. Please see the [bonus exercise](#bonus_dicom) at the end of this lesson
+sample DICOM data for you. Please see the [bonus exercise](#bonus-exercise-dicom-to-nifti) at the end of this lesson
 if you would like to give this a go.
 ::::::::::::::::::::::
 
@@ -786,14 +786,17 @@ As discussed earlier, if you have received medical imaging data from a hosptial
 DICOM format. However, most of the software you are likely to use wants medical images in a 
 more manageable format, typically NIfTI images. There are many ways to convert between the two,
 but probably the most widely used is [dcm2niix](https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage)).
-You can find the sample data in `~/data/ImageDataVisualization/DICOM`
-Let's first change into this directory
+
+You can find the sample data in `~/data/ImageDataVisualization/DICOM`. Let's first change into this directory
+
 ```bash
-cd data/ImageDataVisualization/DICOM
+cd ~/data/ImageDataVisualization/DICOM
 ```
+
 If you list the contents, you will see a single folder called `Subject01`
 
 Let's first make a directory for the Nifti output
+
 ```bash
 mkdir Nifti
 ```
@@ -810,20 +813,24 @@ We covered how to get help for a command in an earlier section.
 
 ::::::::::::::::::::: solution
 1. To get help, we use the -h option:
+
     ```bash
     dcm2niix -h
     ```
 2. The simplest command to do this is 
+   
    ```bash
    dcm2niix -o Nifti Subject01
    ```
 3. To zip the file, we use the -z function:
+   
    ```bash
    dcm2niix -z y -o Nifti Subject01
    ```
-4. TO change the naming structure, we use the -f function. How you name them 
+4. To change the naming structure, we use the -f function. How you name them 
 tends to be your personal choice, and many people choose to use the BIDS
 standard for naming the data. 
+   
    ```bash
    dcm2niix -f %i_%s_%d -z y -o Nifti Subject01
    ```