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6.1_Creating_an_anatomical_ROI

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@[toc](Creating an anatomical ROI) # Step 1: Create mask in FSL 1. Log into a node on HPC: ```bash ssh -X jpfeifer@talapas-ln1.uoregon.edu # followed by the password srun --pty --mem 4000 /bin/bash ``` 2. Open FSLView: ```bash module load fsl fslview ``` 3. Open a standard template brain: Go to File --> Open Standard --> select template (e.g., MNI152_T1_2mm_brain.nii.gz). 4. Activate atlas tools: Go to Tools --> Toolbars --> Atlas tools (new buttons `Atlases` and `Structures` should appear). 5. Click on `Atlases` and make sure your atlases of interest are selected (e.g., Harvard-Oxford subcortical). 6. Click on `Structures` and select your structure of interest for your anatomical ROI. 7. Make sure the two boxes are selected (i.e., Location and Preview) (**Don't close the window just yet!**) 8. Save the image: Go to File --> Save As. # Step 2: Create ROI in SPM
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