Neuroimaging Laboratory Exercise - Lab Manual

Neuroimaging Laboratory Exercise - Lab Manual - Bio 335...

Info iconThis preview shows pages 1–4. Sign up to view the full content.

View Full Document Right Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
This is the end of the preview. Sign up to access the rest of the document.

Unformatted text preview: Bio 335 Neuroimaging 1 LAB Manual: Detailed Instructions for Analyzing PET DATA In this laboratory, you will analyze 4-dimensional neuroimaging data (length, width, depth, and time). You will use software called AMIDE (A Medical Imaging Data Examiner, version 1.0.0) for image analysis (see example window below with labels). PART 1: Viewing the MRI Template in AMIDE 1. Open the desktop link to the Amide software. 2. OPEN the MRI Template by CLICKING ON: File Import File (specify) NIFTI via (x)MedCon Navigate to your data folder on the Desktop double click on the folder [Templates] double click on the file MRI_template.nii (or click open in the window) ignore the AMIDE warning and click OK The study window (white box on the left) now shows a red icon which indicates your MRI template Bio 335 Neuroimaging 2 3. Display the MRI template by clicking (checking) the box next to the red icon. 4. The MRI appears RED automatically; change to traditional grey scale by clicking on: Rainbow scale Color table (hold left click down while you scroll to your color map choice) choose black/white/black by placing the mouse pointer over the option and letting go (it is a color map option near the top of the list, scroll up if necessary to see it) close the window by clicking on the top left x 5. Zoom by clicking on the up arrow or typing in a number. 6. You may notice the image is pixilated (meaning it is not a smooth image). The button can adjust this by changing the interpolation to trilinear. 7. Practice using AMIDE to view images: scroll through the MRI images one view at a time using the slide bars Try holding down the left mouse button, moving it around the image, and releasing it. This will show red cross hairs which will align to the same location in all three views when you release the left click. Use the button to toggle between turning the cross hairs on or off. 8. Locate the CAUDATE, PUTAMEN, NUCLEUS ACCUMBENS and CEREBELLUM with your cross hairs. Question 1 Why are you focusing your analysis on the caudate and putamen? Why do you think the cerebellum may be a good reference region? PART 2: Drawing Regions of Interest (ROIs) 9. Create a new ROI on a coronal section by clicking on: Your region of interest (so it is visible in all three views) Edit Add ROI Ellipsoid type in the name of the ROI, for e.g. Caudate Left Draw the ROI on the coronal plane with either the left or right mouse buttons: o draw-edge-to-edge (LEFT CLICK, HOLD, MOVE the mouse, RELEASE) o draw-center out (RIGHT CLICK, HOLD, MOVE the mouse, RELEASE) Type about 10-30 mm for the depth. You can draw the ROI either way, which ever you prefer. Try to stay within the borders of the region of interest but you can modify the size and location in step 10. Bio 335 Neuroimaging 3 10. Adjusting the position, rotation, and size of ROIs Move your ROI by placing the cursor on the yellow edge of the ROI, the...
View Full Document

Page1 / 12

Neuroimaging Laboratory Exercise - Lab Manual - Bio 335...

This preview shows document pages 1 - 4. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online