DTI Quality Control
Link back to LA5C page.
These are the useable subjects for each group, on each scanner.
Contents
QA Procedures
DTI Analysis Tools and Scripts List
Check Raw DTI Data
Check that the raw DTI data exists for each subject
Run dti_proc.sh Script
dti_proc.sh is a script written by Russ Poldrack, originally for CNP to preprocess raw DTI data. The path for the script is /space/raid2/data/poldrack/CNP/scripts/DTI/dti_proc.sh. The directory structure will need to be adapted for individual projects. The usage is dti_proc <input directory path>.
Note: an alternate version called "dti_proc_regressor" exists. The difference between the two versions is that the regressor script contains a nuisance regressor based on the Galachan, 2010 paper, that we hoped could 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. However, this effort to correct the artifact was unsuccessful and the individuals with vibration artifacts were eliminated.
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 &
For the subject indicated, the script will output the following files in the raw DTI directory:
- B0_image_brain_mask.nii.gz
- B0_image_brain.nii.gz
- B0_image.nii.gz
- dti_diag.pdf
- dtifit_FA2std.nii.gz
- dtifit_FA.nii.gz
- dtifit_L1.nii.gz
- dtifit_L2.nii.gz
- dtifit_L3.nii.gz
- dtifit.log
- dtifit_MD.nii.gz
- dtifit_MO.nii.gz
- dtifit_SO.nii.gz
- dtifit_V12std.nii.gz
- dtifit_V1.nii.gz
- dtifit_V2.nii.gz
- dtifit_V3.nii.gz
- dti_mcf.par
- dti_proc.log
- FA2std.mat
Run DTI_QA.sh Script
To obtain additional QA measures, to supplement the dti_diag.pdf file, then run the DTI_QA.sh script. This script was written by Katie Karlsgodt to produce a text file which checks that the bvals and bvecs match the CNP standards, and calculates the mean MD, mean FA, mean motion, and the maximum motion, and other QA measures.
The path for the script is /space/raid2/data/poldrack/CNP/scripts/DTI//DTI_QA.
The usage is DTI_QA <subjectID> <group>, or dti_proc all <group>.
For example, to run the script on one subject in the CNP schizophrenia group,
1. Run the script, e.g.:
- > dti_proc_temp.sh CNP_50006B SCHZ &
The script will create a dti_report.txt file in the raw DTI directory of the subject.
Check Preprocessed DTI Data
Check Diagnostic Log
After running the dti_proc.sh script, check the diagnostic log for quality assurance of the DTI data:
2. Open the dti_diag.pdf, using the command evince:
- > evince dti_diag.pdf &
3. Check whether the bvals and bvecs match the CNP standards.
Note: across scanners (BMC vs CCN) and within the CCN scanner there were multiple permutations of the 64 direction sequence. All subjects were run using their own directions so the analysis is valid within subject, but they have been flagged so that users are aware if someone does not match the scanner standard.
Alternatively, to run the script on all subjects in the CNP schizophrenia group,
- > dti_proc_temp.sh all SCHZ &
2. Go to the raw DTI directory of the subject, and view the dti_report.txt file, using more or emacs -- Check whether the bvals and bvecs match the CNP standards -- Check degree of cropping. The cerebellum will almost always have the most. If any other regions have more than 10% cropping, check the raw data carefully and rate degree of cropping on the log.
Check for Artifacts
Artifacts included in the CNP data include the Siemen's vibration artifact (indicated by a red blob on the midline in the dorsal posterior part of the brain), blank slices (usually associated with motion) on individual
Check FA Map
After running the dti_proc_regressor.sh script, check the fractional anisotropy (FA) map for quality assurance:
1. Log on to func and go to the directory /space/raid2/data/poldrack/CNP/${group}/CNP_{subjectID}/raw/DTI_64DIR_*:
- > ssh $username@funcserv1
- > cd /space/raid2/data/poldrack/CNP/${group}/CNP_{subjectID}/raw/DTI_64DIR_*
- > ls
2. Open the FA map in FSLView:
- > fslview dtifit_FA.nii.gz &
3. Check if the FA map includes the entire brain and if the FA map looks unusual or not, and log this in the CNP DTI QA Google Document.
Check Color Map
After running the dti_proc.sh script, check the color map for quality assurance:
1. Log on to func and go to the directory /space/raid2/data/poldrack/CNP/${group}/CNP_{subjectID}/raw/DTI_64DIR_*:
- > ssh $username@funcserv1
- > cd /space/raid2/data/poldrack/CNP/${group}/CNP_{subjectID}/raw/DTI_64DIR_*
- > ls
2. Open both the FA and color maps in FSLView (or add the color map to FSLView, if you are already viewing the FA map):
- > fslview dtifit_FA.nii.gz dtifit_V1.nii.gz &
The FSLView GUI will display these files as:
3. To view the color map, select the dtifit_V1 file, and press the "i" button. An "Overlay Information Dialog" window will appear. For "Display as:", select "RGB" and for "Modulation:", select "dtifit_FA". Close this window.
4. The color map should now display as:
5. Check if the directions of the major fiber tracts are colored appropriately by scrolling through the slices. In the coronal view, the corticospinal tract (superior-inferior) should be blue. In the sagittal view, the corpus callosum (right-left) should be red. In the axial view, the anterior-posterior tracts should be green.
Also, check if the color map includes the entire brain and if the color map looks unusual or not. Log this in the appropriate google doc.
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