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| =Quality Control= | | =Quality Control= |
− | The checking procedures for CNP follow the Cannon Lab DTI QA Protocol, which was adapted from procedures in Paul Thompson's lab.
| + | A complete description of the QA can be found at [[DTI_QA]] |
− | | + | |
− | ==DTI_QA script==
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− | The additional QA script is located at /space/raid2/data/poldrack/CNP/scripts/DTI_QA.sh
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− | | + | |
− | ===Usage===
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− | The usage is DTI_QA <subjectID> <group>, or dti_proc all <group>.
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− | | + | |
− | For example, to run the script on one subject in the CNP schizophrenia group,<br/>
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− | 1. Log on to func and go to the directory /space/raid2/data/poldrack/CNP/scripts:
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− | :> ssh $username@funcserv1
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− | :> cd /space/raid2/data/poldrack/CNP/scripts
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− | | + | |
− | 2. Run the script, e.g.:
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− | :> dti_proc_temp.sh CNP_50006B SCHZ &
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− | | + | |
− | 3. Alternatively, to run the script on all subjects in the CNP schizophrenia group,<br/>
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− | :> dti_proc_temp.sh all SCHZ &
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− | | + | |
− | ===Script Actions===
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− | This script creates a small text file to be used in QA. If the script runs properly it:<br/>
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− | 1. matches bvals and bvecs<br/>
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− | 2. calculates mean in-mask FA and MD<br/>
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− | 3. calculates motion in each direction<br/>
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− | 4. creates a standard deviation file for regular and mcf images<br/>
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− | 5. uses regional masks to calculate the percentage of cropped voxels in the occipital lobe, frontal lobe, superior region, temporal lobes and cerebellum.<br/>
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− | | + | |
− | ===Output===
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− | The script will create a <b>dti_report.txt</b> file in the raw DTI directory of the subject.
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− | | + | |
− | ==How to Do QA==
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− | ===Check Diagnostic Log===
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− | After running the dti_proc.sh script, check the diagnostic log for quality assurance of the DTI data:<br/>
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− | 1. Log on to func and go to the directory, for example, /space/raid2/data/poldrack/CNP/${group}/CNP_{subjectID}/raw/DTI_64DIR_*:
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− | :> ssh $username@funcserv1
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− | :> cd /space/raid2/data/poldrack/CNP/${group}/CNP_{subjectID}/raw/DTI_64DIR_*
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− | :> ls
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− | | + | |
− | 2. Open the dti_diag.pdf, using the command <b>[[Basic UNIX Commands#evince | evince]]</b>:
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− | :> evince dti_diag.pdf &
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− | | + | |
− | 3. Check whether the bvals and bvecs match the CNP standards, and log this in the [https://spreadsheets.google.com/ccc?key=0AhLKRRgAIOCVdG9rY0szNFppcGZ0QmF3ejBYLUY5S0E&hl=en#gid=0 CNP DTI QA Google Document].
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− | | + | |
− | 4. Go to the raw DTI directory of the subject, and open the dti_report.txt file, using the command <b>[[Basic UNIX Commands#emacs | emacs]]</b>:
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− | :> cd /space/raid2/data/poldrack/CNP/SCHZ/CNP_50006B/DTI_64DIR_3
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− | :> ls
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− | :> emacs dti_report.txt &
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− | | + | |
− | 5. Check whether the bvals and bvecs match the CNP standards, and log this in the [https://spreadsheets.google.com/ccc?key=0AhLKRRgAIOCVdG9rY0szNFppcGZ0QmF3ejBYLUY5S0E&hl=en#gid=0 CNP DTI QA Google Document].
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− | | + | |
− | ===Check for Artifacts===
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− | Artifacts observed in this data set include-
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− | :-missing slices- this would be on only one volume, and consist of an entire isolated missing horizontal slice
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− | :-vibration artifact (only on BMC subjects)- this usually shows as a red patch directly on the midline, primarily in the parietal region
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− | :-striping
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− | :-cropping
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− | | + | |
− | ===Check Raw Data===
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− | ====Check FA Map====
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− | After running the dti_proc_regressor.sh script, check the fractional anisotropy (FA) map for quality assurance:<br/>
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− | 1. Log on to func and go to the directory /space/raid2/data/poldrack/CNP/${group}/CNP_{subjectID}/raw/DTI_64DIR_*:
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− | :> ssh $username@funcserv1
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− | :> cd /space/raid2/data/poldrack/CNP/${group}/CNP_{subjectID}/raw/DTI_64DIR_*
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− | :> ls
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− | | + | |
− | 2. Open the FA map in FSLView:
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− | :> fslview dtifit_FA.nii.gz &
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− | | + | |
− | 3. Check if the FA map includes the entire brain and if the FA map looks unusual or not
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− | | + | |
− | ====Check Color Map====
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− | After running the dti_proc.sh script, check the color map for quality assurance:<br/>
| + | |
− | 1. Log on to func and go to the directory /space/raid2/data/poldrack/CNP/${group}/CNP_{subjectID}/raw/DTI_64DIR_*:
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− | :> ssh $username@funcserv1
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− | :> cd /space/raid2/data/poldrack/CNP/${group}/CNP_{subjectID}/raw/DTI_64DIR_*
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− | :> ls
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− | | + | |
− | 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):
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− | :> fslview dtifit_FA.nii.gz dtifit_V1.nii.gz &
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− | | + | |
− | 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.
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− | 4. The color map should now display with a dark background and red/blue/green tracts.
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− | 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.
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− | | + | |
− | 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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− | | + | |
− | ====Check for Cropping====
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− | In the output from the DTI_QA script is a number for each of a set of regions (cerebellum, superior, temporal, frontal). This number represents the percentage of voxels missing in that region. If the number is greater than about 10, you should go back and look at the FA map to make sure that actual tract data is not missing (some small percent, which would usually represent grey matter, can be missing off the edges without much effect). There will always be a large percentage of cerebellum voxels missing, but this can be ignored.
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− | | + | |
− | ====Watch raw data as movie====
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− | Load up the raw data file (like DTI_64dir_7.nii.gz) into fslview, and watch through each volume as a movie. It is normal for the first volume to be much brighter, that is the B0 image.
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− | | + | |
− | ==QA Rating System==
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− | After logging the intermediate steps in the google doc, a final rating can be calculated. This is based on:
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− | :1. Coverage flag (based on cropping measures rated 0=no cropping, 1=minor cropping, 2=severe unusable cropping)
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− | :2. Motion flags (based on watching raw data as movie, and on pdfs).
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− | :3. Tensor direction flags (based on bvals and bvecs and color map)
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− | :4. Artifact flags
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− | | + | |
− | The overall Quality score is generated from these measures and varies from 1-4.
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− | :1=excellent
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− | :2=good (useable, but depending on analysis might want to take a look at reason for score)
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− | :3=fair (useable, but depending on analysis might want to take a look at reason for score)
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− | :4=unusable (all individuals with vibration artifacts are in this category, along with any others with irreconcilable problems)
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− | :-1= not evaluated
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− | | + | |
− | The scores and reasons for them are available on the HTAC database.
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− | [[File:DTI_Rankings.png]] | + | |
− | | + | |
− | | + | |
− | | + | |
− | ----
| + | |
− | Link back to [[LA5C]] page. <br/>
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− | Return to [[CNP]]
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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.
2. Find the path of the raw DTI directory for one subject, and run the script, e.g.:
The dti_proc script processes the data using FSL Diffusion Toolbox (FDT).
6. Motion is calculated
7. bvecs and bvals for each subject are compared to the CNP standards.
7. a pdf is generated (dti_diag.pdf)
For the subject indicated, the script will output the following files in the raw DTI directory: