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. ls ../../../nii/

• This command will list the NIfTI volume image files for the particular subject while remaining in the subject's unfold directory.

4. Find the file that has "hhr_struct" in its name and copy the whole NAME

5. NLF_InitVol(",'../../../nii/NAME');

• The file name that you copied should be in place of NAME. This command will