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Source  : 1085750
Branch  : main
Author  : davecash75 <[email protected]>
Time    : 2024-09-23 09:48:16 +0000
Message : Merge pull request #7 from HealthBioscienceIDEAS/4-add-quick-dcm2niix-intro

Stray commit that wasn't done before

imaging-data-structure-and-formats.md

@@ -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
    ```

md5sum.txt

@@ -4,7 +4,7 @@
 "config.yaml" "389c02e39e8db66235f1309d40d808d5" "site/built/config.yaml" "2024-09-23"
 "index.md" "764911ed72d8ae6bf96758c79c2604b7" "site/built/index.md" "2024-09-23"
 "links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2024-09-23"
-"episodes/imaging-data-structure-and-formats.Rmd" "80dba281816fcf3be055257f2f03c2bd" "site/built/imaging-data-structure-and-formats.md" "2024-09-23"
+"episodes/imaging-data-structure-and-formats.Rmd" "75c2d6d6c5e6a682c69a404d04a440ee" "site/built/imaging-data-structure-and-formats.md" "2024-09-23"
 "episodes/structural-mri.Rmd" "c3e33d9fde6503262ee2b2b148829f10" "site/built/structural-mri.md" "2024-09-23"
 "episodes/pet-imaging.Rmd" "b301a5ca69801d55b37c5401179e8f47" "site/built/pet-imaging.md" "2024-09-23"
 "episodes/diffusion-weighted-imaging.Rmd" "0e0dfe9ad5eb39fe02af3527770fa080" "site/built/diffusion-weighted-imaging.md" "2024-09-23"