Segmentation

Creating Segmentation Files

Segmentation files are created by first creating vAnatomy.dat files in Matlab. To open Matlab in Terminal you must be logged into hoffman. Once you are logged on, you will run these commands in Terminal:

1. qrsh -l i,h_rt=5:00:00,h_data=4G

• The "5:00:00" indicates that Matlab will run for 5 hours.

2. module load matlab/7.14

3. matlab

To create the vAnatomy.dat file and prepare the high resolution T2 images, you will run these following commands in Matlab:

1. addpath(genpath('/u/home/FMRI/apps/unfolding/current/'));

• Note: The warning message can be ignored.

2. cd /u/project/sbook/data/AD/subjects/AD_1XXXX/20######/analysis/structural/unfold

• X's denote the subject number and # indicates scan date. Running this command will take you to the subject's unfold directory.

3. NLF_InitVol

• This command will begin initializing the volume anatomy file.

4. In the window that appears, navigate to the subject's "nii" directory of NIfTI volume image files and select the "hhr_struct" file.

5. Another window with the image scan of the subject will appear. Begin drawing a rectangular box around the hippocampal region, covering both the left and right sides.

• Note: It is important to draw the rectangle with enough vertical space above and below the region to account for height changes in different slides.

6. Once the box has been drawn, double click inside the drawn region and Matlab will begin creating the file.