UW_USAGE.txt

This software will extract mean FA values for each subject in a TBSS dataset.


Before using, please ensure that:

1. DTI data for all subjects has been preprocessed (all steps below should be complete):
	a. Converted to NIFTI
	b. Skull-stripped
	c. Corrected for motion and eddy current-induced distortions
	d. Tensor fit to produce FA image
	e. QA checks of SNR and motion to ensure subject meets criteria for inclusion

2. All images that passed QA check have been added to TBSS directory (preferably with [SubjectID]_FA.nii.gz name)

3. The UW_ENIGMA_TBSS.sh and UW_ENIGMA_ROI.sh scripts have been edited and saved:
	a. PROJECT_DIR and DTI_DIR likely will need to be changed
	b. The pattern for subject files (in UW_ENIGMA_TBSS.sh) may need to be edited also


To run the ROI analyses:

1. Run the UW_ENIGMA_TBSS.sh script to run first three steps of TBSS (preprocessing, registration, and post-registration):
	bash /mnt/stressdevlab/scripts/ROI/enigma/UW_ENIGMA_TBSS.sh

2. Double-check the FASubs.txt and FADirs.txt files to confirm that they match TBSS directory structure

3. Run the UW_ENIGMA_ROI.sh script to run ENIGMA C++ scripts that will create table of values for all subjects (63 ROIs each):
	bash /mnt/stressdevlab/scripts/ROI/enigma/UW_ENIGMA_ROI.sh