Skip to content

Commit

Permalink
Minor corrections
Browse files Browse the repository at this point in the history
  • Loading branch information
pzeidman authored May 19, 2024
1 parent 4001316 commit da4097c
Show file tree
Hide file tree
Showing 2 changed files with 8 additions and 6 deletions.
2 changes: 1 addition & 1 deletion docs/tutorials/vbm/image_processing.md
Original file line number Diff line number Diff line change
Expand Up @@ -273,7 +273,7 @@ Ashburner, J., 2009. "Computational anatomy with the SPM software". *Magnetic Re
<div>

Mechelli, A., C.J. Price, K.J. Friston and J. Ashburner. 2005. "Voxel-Based Morphometry of the Human Brain: Methods and Applications." *Current Medical Imaging Reviews* 1:105--113.
<https://doi.org/10.2174/1573405054038726>.
<https://www.fil.ion.ucl.ac.uk/spm/doc/papers/am_vbmreview.pdf>.

</div>

12 changes: 7 additions & 5 deletions docs/tutorials/vbmcourse24/index.md
Original file line number Diff line number Diff line change
@@ -1,9 +1,11 @@
# Voxel Based Morphometry Tutorial using the Geodesic Shooting Toolbox

## Requirements
This tutorial assumes you have:

- T1w MRI data for two groups (suggest ~10 subjects in each group)
- Basic demographic details for each subject (Age, Gender + any other covariates)
- MATLAB running SPM12. Make sure SPM12 and all subdirectories is in the MATLAB path (test by typing “which spm” in MATLAB prompt)
- MATLAB running SPM12. Make sure SPM12 and all subdirectories are in the MATLAB path (test by typing “which spm” in MATLAB prompt)

![](../../assets/figures/tutorials/vbm_spm_course_2024/index_dir_structure.png)

Expand All @@ -13,14 +15,14 @@ This tutorial will go through the full processing pipeline for a two group VBM a
![](../../assets/figures/tutorials/vbm_spm_course_2024/index_workflow.png)

## Notes on the SPM VBM demo data
For the SPM workshop, a demo analysis looking for left-right brain asymmetry will be performed. This data consists of 12 R1 maps (1/T1) that have also been left-right flipped providing a total cohort size of 24. These have already been dicom imported and are supplied as native space .nii files.
For the SPM course at UCL, a demo analysis looking for left-right brain asymmetry will be performed. This data consists of 12 R1 maps (1/T1) that have also been left-right flipped providing a total cohort size of 24. These have already been DICOM imported and are supplied as native space .nii files.
To speed up the demo, folders are organized into:

- day_1/02_preprocessing_asymmetry/01-Start: This is where you begin to run the whole thing
- day_1/02_preprocessing_asymmetry/01-Start: This is where you begin to run the whole analysis
<!-- - Middle: Spm segment completed, ready for shoot warping -->
- day_2/03_group_level_asymmetry/03-End: Completed warped, modulated data ready for VBM analysis

To note, if you just run the pipeline on all the data in “start”, that will output all of the data in the raw folder, for each subject. You can then double check what you find with the actual end result.
Note, if you just run the pipeline on all the data in the folder “01-Start”, that will output all of the data in the raw folder, for each subject. You can then double check what you find with the actual end result.

The <!--‘middle’ and-->end’ folder has data re-organised to more closely follow how it would be structured in a BIDS dataset. This means all the various outputs can be found in the derivatives folder.
The <!--‘middle’ and-->03-End’ folder has data re-organised to more closely follow how it would be structured in a BIDS dataset. This means all the various outputs can be found in the derivatives folder.

0 comments on commit da4097c

Please sign in to comment.