AD: ANTs

Prior to following these instructions, install Windows Subsystem for Linux (i.e. WSL) and then install Ubuntu. Also install ITK-SNAP and MRICroGL.

1. Follow the instructions in the 'ANTs Installation' confluence page: https://osabrainresearch.atlassian.net/wiki/spaces/AN/pages/2623504387

2. Make a new folder named Analysis_ANTs_Test, with a ‘projects’ folder, a ‘stats’ folder and a subfolder called ‘CONTROL’ in the ‘projects’ folder.

3. Copy in a few of your subject folders into the ‘CONTROL’ folder. Also make sure to copy in your ‘method’ file into the ’metadata' folder in each subjects' DTI folder.

4. In the following directory, make a folder and name it ‘rats_mri_project’: \\wsl.localhost\Ubuntu\home\*your user folder*. Note - If you are able to access the ‘root’ folder in your ‘Ubuntu’ folder, make this ‘rats_mri_project’ folder in the ‘root’ folder, instead of the ‘home’ folder.

5. Open CSPM → Preclinical.

6. In the ‘Main’ tab, tick the ‘VBM’ and ‘DTI’ boxes.

7. In the ‘Setup’ tab, make sure ‘Rat’ is selected (with a scale factor of 8), paste your ‘projects’ folder path into the ‘Project folder’ box, the folder path of your ‘rats_mri_project' into the ‘Linux folder’ box and the folder path of your ‘stats' folder into the ‘Stats’ box. E.g.

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8. In the ‘VBM’ and ‘DTI’ tabs, enter your voxel size and desired smoothing kernel size.

9. Click the ‘ANTs In-n-Out’ button.

10. Once ‘ANTs In-n-Out’ has finished running, go through each subjects’ folder in the ‘subjects’ folder of your ‘rats_mri_project’ folder and open the images with the suffixes ‘BrainExtractionBrain’, ‘BrainExtractionMask’ and ‘InverseWarped’, side by side. Note- these images are in GZ file format. You don’t have to convert them to nifti format to view them. Simply drag and drop them into MRIcroGL windows.

11. Also open the SIGMA template (or anatomical mean, if you have decided to run ANTs after running ‘Preprocess after Coreg’), next to the above images.

12. Compare the three images to the SIGMA template. This is an example of a subject for which the brain was extracted properly:

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13. If you find a subject for which the brain was not extracted properly, e.g.

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    read the instructions on page https://osabrainresearch.atlassian.net/wiki/spaces/AN/pages/2623733772 for how to use ITK-SNAP to improve brain extraction.

14. Then re-run ‘ANTs In-n-Out’.

15. Go through and check the ‘BrainExtractionBrain’, ‘BrainExtractionMask’ and ‘InverseWarped’ images for subjects which you masked in ITK-SNAP, to check their brains were extracted properly.

16. If it works on this sub-set of your subjects, go ahead and paste the folder path of your analysis folder with all your subjects in it, into the ‘Preclinical’ GUI and click ‘ANTs In-n-Out’. Then repeat steps 10-15.

17. You can now analyse your data by following the instructions in the https://osabrainresearch.atlassian.net/wiki/spaces/AN/pages/2627109034/AD+Data+Analysis+and+Visualisation?atlOrigin=eyJpIjoiMTZiODQ0OWJkMmNiNGM1NTkxZTRjZDUyOWRmMDE5Y2MiLCJwIjoiYyJ9 page.