Anatomy exercise lab
From NITP Summer Course Wiki
Part 0 (Optional)
In this part of the lab you will brush up (or learn) anatomical structures using the Interactive Neuroanatomy Tools from the University of Washington. For each of these, you should first study the anatomy of the region by clicking "Show All Outlines" to outline all of the structures, and then clicking "Label All" to see labels for all of these outlined structures. Once you have studied the anatomy, you should test yourself using the "Start Quiz" button.
Here are some sample links:
Horizontal Sections:
Saggital sections
Part 1
In this part of the exercise you will examine a real fMRI dataset, localize the activation, and construct a table like one would see in an fMRI paper.
Go to /users/psych254/FSL/anat_exercise_data/ and load mean_anat and then zstat1_clustered into FSLview. Launch FSLview by clicking on the "X11.app" icon in the dock (it looks like a grey X on a white square), and typing fsl into the white terminal window that appears. Click on the FSLview button on the bottom of the main FSL program once it comes up on the screen. Load the aformentioned files by going to "File -> Open" and "File -> Add" from the top menu. The program will probably default to the user home directory, which is /users/psych254/, so you can go from there to find the dataset. Set the min value in the upper window to 3. Your goal is to describe the activation in this map. The following is a list of clusters of activation. For each of these clusters, you should determine which brain regions are included in the cluster. Note that some of the clusters are quite large, so be sure to get all regions within a cluster.
| # of voxels | Maximum Z | X (mm) | Y (mm) | Z (mm) |
|---|---|---|---|---|
| 2161 | 4.45 | 32 | -68 | -26 |
| 1588 | 4.8 | -14 | -12 | -6 |
| 1343 | 5.23 | 22 | -102 | -6 |
| 924 | 4.49 | -44 | -28 | 48 |
| 840 | 4.72 | 28 | 2 | -4 |
| 311 | 4.66 | -34 | -62 | -38 |
| 241 | 4.36 | 44 | 42 | 16 |
| 226 | 4.05 | -10 | -4 | 58 |
| 218 | 4.29 | 32 | -52 | -60 |
| 104 | 4.58 | -60 | 6 | 24 |
| 74 | 3.85 | -42 | -78 | -30 |
After doing your best to identify the regions yourself, you can see how closely your identifications were to a standardized probabilistic atlas by going to the "Tools" menu, and selecting "Atlas Tools" from the "Toolbar" sub-menu. This will add another box to the bottom of FSLView that contains the probabilities of various ROIs at each voxel based on the Harvard-Oxford Atlas.
