Copy of Lab 10 Instructions

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Dec 6, 2023

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Lab 10 - Face-Occupation Pairs Analysis ● Today we will be getting the results of the face-occupation pairs ● You will need the results files for both words and face-occupation pairs (you should already have word pairs file) and you will need to grab images of the left and right hemispheres for both the hippocampus and the fusiform gyrus, for both word and face-occupation pairs! ● You’ll need 8 screenshots to use/refer to for your results/paper: (2 regions x 2 hemispheres x 2 conditions). ● For today's lab you will submit the face-occupation results you get in Excel format and your answer sheet for Part 4. Instructions Research Question for Paper: How does the brain response differ when encoding word pairs compared to face-occupation pairs? Part 1 - Matlab Setup 1. Before starting, you need to download and unzip the folder of data files from Canvas. 2. You can double click the file you downloaded from Canvas (“fMRI_lab_files.zip”) to unzip it into a folder full of files. 3. There are two subfolders - “data” and “”jspm_view_v1.4” - that you should move to your desktop before proceeding. 4. Start Matlab you can simply hit ‘command’ + ‘space’, then type “matlab” and hit ‘enter’. A couple icons should bounce around for a bit, but eventually the program will pop up. 5. Now, we need to show matlab where the ‘jspm_view_v1.4’ folder is located. This folder contains the viewing software that we’ll be using to visualize the fMRI data. Enter the following command into the Matlab command window (copy all but quotes, and past into matlab): ‘addpath ~/Desktop/jspm_view_v1.4’ 6. Now, we need to move our relative location within the Matlab session to the ‘data’ folder we just copied over. You can do this by entering the following command into the Matlab command window: ‘cd ~/Desktop/data’ 7. Finally, we’ll start the viewing software ‘jspm_view’ by using the following command in the Matlab command window: ‘jspm_view’ 8. Wait about 10 seconds to allow the program to fully load before starting the lab exercise.

Part 2 - Word Pairs Analysis (IF NEEDED) ● You may have this from the last lab. If you already completed the Lab 9 assignment, skip this part and move on to Part 3. Otherwise, follow the instructions listed below. ● Make sure your file has 40 (or 39) active regions – shown at the bottom of the sheet. ○ If you do not, you will need to go through steps from the previous lab to get this data again. ● See below about how to find the correct coordinates to visualize your region of interest for screenshots 1. Select "Load Image" (upper left button), 2. Select the "wSPGR.hdr" file. 3. Change the "Select L/R" switch to "On" (upper right button), so left is shown on left and right on right. 4. Next we will load a statistical map from the "words" experiment. Select "Load Overlay SPM" (upper middle button) 5. select the "spmT_N_e-c.hdr" file from within the "words" data folder. 6. Set the "Positive Threshold" to 4.03 7. Set the "Min cluster size" to 34. Hit apply ○ This gives us a predetermined "Family Wise Error" (FEW) rate (meaning error rate across all voxels) of p < .05. ○ So now we can expect only 5% of the ‘active regions’ to be significant by chance, so the results will be more trustworthy 8. Open the "data" folder in the finder, you should have a new file called " spmT_N_e- c_AALactive_num_thr4.03.txt". 9. Select ‘open with’ and choose Excel. 10. Separate the data into columns by first selecting all of column ‘A’ by clicking on the ‘A’ in the upper left hand corner. This should highlight all of the cells in column A. 11. Then select the menu item ‘Data->Text to Columns…’. From here choose ‘Fixed Width’, and click ‘Finish’. The data should now be sorted into 4 columns. The data in each column 1-4 is as follows: 1. Region label. 2. The number of active voxels within the region (and percentage of within- region voxels that are active). 3. The t-value of the most active voxel within the region. 4. The XYZ coordinate location of the most active voxel: X = left (negative) to right (positive) Y = caudal (negative) to rostral (positive) Z = inferior (negative) to superior (positive)

1. Your words file should contain 40 (or 39) active regions. 2. Rename this file so you know this is the data for the word pairs condition. 3. Use the coordinates from the results file to navigate to the location of your brain region of interest in the brain viewer windows (with "Crosshairs On"). ○ The results file has the coordinates in mm, but the "Loc(MNI:Voxel)" fields of the brain viewer are in voxels. ○ Since each voxel is 2 mm, you need to divide each of the results file coordinates by 2 before entering them into the brain viewer window. ○ For example, if the results file said "10, 20, 30" you would enter "5, 10, 15" (X, Y, Z order) into the viewer window. Part 3 - Face-Occupation Pairs Analysis ● This is new data you did not investigate in the last lab. ● These instructions are exactly the same as above, except you will overlay the SPM image from the faces folder. 1. Select "Load Image" (upper left button). 2. Select the "wSPGR.hdr" file. 3. Change the "Select L/R" switch to "On" (upper right button), so left is shown on left and right on right. 4. Next we will load a statistical map from the "faces" experiment. Select "Load Overlay SPM" (upper middle button). 5. Select the "spmT_N_e-c.hdr" file from within the "faces" data folder. 6. Set the "Positive Threshold" to 4.03. 7. Set the "Min cluster size" to 34. Hit apply. 1. This gives us a predetermined "Family Wise Error" (FEW) rate (meaning error rate across all voxels) of p < .05. So now we can expect only 5% of the ‘active regions’ to be significant by chance, so the results will be more trustworthy 8. Open the "data" folder in the finder, you should have a new file called "spmT_N_e- c_AALactive_num_thr4.03.txt". 9. Select ‘open with’ and choose Excel. 10. Separate the data into columns by first selecting all of column ‘A’ by clicking on the ‘A’ in the upper left hand corner. This should highlight all of the cells in column A. 11. Select the menu item ‘Data->Text to Columns…’. From here choose ‘Fixed Width’, and click ‘Finish’. The data should now be sorted into 4 columns. The data in each column 1-4 is as follows: 1. Region label. 2. The number of active voxels within the region (and percentage of within-region voxels that are active).

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3. The t-value of the most active voxel within the region. 4. The XYZ coordinate location of the most active voxel: X = left (negative) to right (positive) Y = caudal (negative) to rostral (positive) Z = inferior (negative) to superior (positive) 1. Your face-occupation file should contain 48 active regions. For today's lab, please save the face-occupation results you get in Excel format. 2. Rename this file so you know this is the data for the face-occupation pairs condition. Part 4 1. Using results in your Excel spreadsheet, paste all 4 results columns from the left and right hippocampus into your submission document. (#11) - ○ Use the coordinates from the results file, to navigate to the location of the left hippocampus in the brain viewer windows (with "Crosshairs On"). ○ The results file has the coordinates in mm, but the "Loc(MNI:Voxel)" fields of the brain viewer are in voxels. ○ Since each voxel is 2 mm, you need to divide each of the results file coordinates by 2 before entering them into the brain viewer window. ○ For example, if the results file said "10, 20, 30" you would enter "5, 10, 15" (X, Y, Z order) into the viewer window. ○ Do this to find the location of the left hippocampus. ○ Grab and paste a picture of the results. -

○ Repeat these steps for the right hippocampus. - 2. Based on what you know about the hippocampus, how would you interpret these results? Make sure to compare left and right activation. - The Left Hippocampus has about 450 voxels which accounts for 47.47% of the total active voxels in the left hippocampus. The Right Hippocampus has 256 voxels which accounts for 26.81% of the total active voxels in the right hippocampus. - I would say the Left hippocampus is more active than the right hippocampus is which shows that the cognitive process associated with memory and spatial navigation is more active in the left hippocampus than in the right hippocampus. 3. Repeat steps 1 & 2 for the left and right fusiform (try "Crosshairs Off" if activity is hard to see).

- - Left Fusiform - - Right Fusiform 4. Based on what you know about the fusiform gyrus, how would you interpret these results? Make sure to compare left and right activation. - The Left Fusiform has 644 voxels which takes up approximately 27.95% of the total activation voxels. - The Right Fusiform has 319 voxels which takes up 12.59% of the total activation voxels. - Based off these results, the left fusiform exhibits higher activation with 644 active voxels which suggests that visual processing (related to face and object recognition) is more noticeable in the left hemisphere which is an indication of

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hemispheric lateralization. Please save your answer sheet as a ‘.pdf’ or ‘.docx’ file and upload your responses to Canvas along with the face occupation results you’ve found as an Excel (.xlsl) file.

Copy of Lab 10 Instructions

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