Skip to content

Commit 40a5914

Browse files
committed
Documentation: Unsure how to properly make the pictures smaller, I literally made the pictures smaller
1 parent 44804c9 commit 40a5914

13 files changed

+7
-6
lines changed
Loading
Loading
Loading
Loading
Loading
Loading
Loading
Loading
Loading
Loading

docs/tutorials/vbmcourse24/data_prep.md

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
# Data preparation
22

3-
## 1. Setting up the directory structure
3+
## Setting up the directory structure
44

55
Neuroimaging experiments result in complicated data that can be arranged in many different ways. Historically, individuals have tended to use their own unique naming/directory structures. The “Brain Imaging Data Structure” (BIDS) Specification has been designed to standardise this to help others understand the data, aiding replication, data-sharing and collaborations. For more details see: https://bids.neuroimaging.io/
66

@@ -10,7 +10,7 @@ For this demo, we will use the anatomical and naming convention as per BIDS:
1010

1111
See the end of this section for a code snippit to combine this with dicom import.
1212

13-
## 2. DICOM import
13+
## DICOM import
1414

1515
Normally, MRI data comes from the scanner in dicom file format (`.dcm`). To use this we first need to import the data and convert it into nifti file format. It is preferable to use “single file nifti format” rather than two-file (`.img` and `.hdr`).
1616

@@ -71,4 +71,5 @@ end
7171
end
7272
7373
clear X group sub bidsanatomy data matlabbatch target study
74-
```
74+
```
75+

docs/tutorials/vbmcourse24/preprocessing.md

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
22

33
Here is an overview of the structural pre-processing steps we are aiming to achieve:
44

5-
![](../../assets/figures/tutorials/vbm_spm_course_2024/preprocessing_workflow.png)
5+
#![](../../assets/figures/tutorials/vbm_spm_course_2024/preprocessing_workflow.png)
66

77
!!! tip "Important before starting"
88
While the SPM pipelines do an excellent job of combining and realigning data, they do rely on the source data (i.e. all of the T1w MRIs in native subject space) being in reasonably close alignment to one another.
@@ -206,4 +206,4 @@ for i=1:Sw,
206206
spm_jobman('run',matlabbatch);
207207
end
208208
end
209-
```
209+
```

mkdocs.yml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -99,7 +99,7 @@ nav:
9999
- 'Factorial': 'tutorials/fmri/group/factorial.md'
100100
- 'VBM':
101101
- 'Getting started': 'tutorials/vbmcourse24/index.md'
102-
- 'Data preparation': 'tutorials/vbmcourse24/data_prep.md'
102+
#- 'Data preparation': 'tutorials/vbmcourse24/data_prep.md'
103103
- 'Preprocessing': 'tutorials/vbmcourse24/preprocessing.md'
104104
- 'Analysis': 'tutorials/vbmcourse24/analysis.md'
105105
#- 'Getting started': 'tutorials/vbm/index.md'

0 commit comments

Comments
 (0)