The DTI was acquired using a 64 direction sequence. Parameters were: 2mm slices, TR/TE=9000/93, 1 average, 96x96 matrix, 90 degree flip angle, axial slices, b=1000.
dti_proc.sh is a script written by Russ Poldrack to preprocess the raw CNP DTI data. The path for the script is /space/raid2/data/poldrack/CNP/scripts/dti_proc.sh.
To run the script on an entire subject group (CONTROLS, SCHZ, BIPOLAR, ADHD) use the wrapper script run_dti_proc.sh
NOTE: An alternate version exists called dti_proc_regressor. The difference between the two versions is that the regressor script contains a nuisance regressor based on the Galachan, 2010 paper, that can to some extent correct for vibration artifacts. This artifact exists on BMC data before Fall 2010. After Fall 2010 the table was bolted down, correcting the artifact. The CCN table was bolted at installation, thus avoiding the artifact entirely. Unfortunately it does not entirely correct the issue, so the shareable data uses the original version of the script with people who show the artifact marked for elimination.
For example, to run the script on one CNP subject,
1. Log on to func and go to the directory /space/raid2/data/poldrack/CNP/scripts:
- > ssh $username@funcserv1
- > cd /space/raid2/data/poldrack/CNP/scripts
2. Find the path of the raw DTI directory for one subject, and run the script, e.g.:
- > dti_proc /space/raid2/data/poldrack/CNP/SCHZ/CNP_50006B/raw/DTI_64DIR_3 &
The dti_proc script processes the data using FSL Diffusion Toolbox (FDT).
1. B0 image is skull stripped, creating B0_image_brain
2. the raw data are registered to the first (B0) image using mcflirt- this both corrects for eddy currents and helps motion, the resulting file is dti_mcf
3. dtifit is run, creating FA, L1, L2, MD and other processed images in subject space
4. the FA and color maps are registered to MNI space (FA2std and V12std).
5. Generic ROIs from the JHU atlas are applied to the FA image in standard space.
- WARNING- the resulting values are NOT to be used as data, rather just as first pass markers for scan integrity. They are not well registered enough to be used for anything, as evidenced by the low FA values.
6. Motion is calculated
7. bvecs and bvals for each subject are compared to the CNP standards.
- NOTE: there are different bvecs and bvals for subjects on the CCN and BMC scanners, as well as for a subset of subjects scanned during the transition and intial set up of the CCN
7. a pdf is generated (dti_diag.pdf)
For the subject indicated, the script will output the following files in the raw DTI directory:
A complete description of the QA can be found at DTI_Quality_Control