XNAT user documentation
Tagging your scans
For BOLDQC to discover BOLD scans to process, you need to set the scan type in XNAT
Type |
Example series |
|---|---|
BOLD |
|
The image below displays an MR Session report page with populated types
Running the pipeline
To run the BOLDQC pipeline, use the Run Containers > boldqc-session button located within the Actions box on the MR Session report page
Note
If you don’t see the Run Containers menu, please refer to Setting up the container.
This should bring up a small form with any configurable settings. Continue reading for a description of each setting
run
Note
The run number is not the scan number. If scan 17 was the first
BOLD scan within the MR session, the run number would be 1, the
second BOLD scan would be run 2, and so on.
This should be set to the integer value of the BOLD scan you want to process.
Understanding the report page
The following section will break down each section of the BOLDQC report page.
Left pane
The left pane is broken up into several distinct sections. Each section will be described below.
Summary
The Summary pane orients the user to what MR Session they’re currently looking at and various processing details
Key |
Description |
|---|---|
MR Session |
MR Session label |
Processed |
Processing date |
BOLD scan |
Processed BOLD scan |
Parameters
The Parameters pane displays fine-grained scan information
Key |
Description |
|---|---|
Num Volumes |
Number of time points |
Num Voxels |
Number of voxels included in the analysis |
Mask Threshold |
Masking threshold |
Skip |
Number of initial time points discarded |
QC Metrics
The QC Metrics pane displays quality control metrics computed over the entire volume
Metric |
Description |
|---|---|
Mean |
Mean signal intensity |
StDev |
Mean voxel Standard deviation |
Slice SNR |
Mean slice-based SNR (sensitive to motion) |
Voxel SNR |
Mean voxel SNR |
Mean Rel Motion |
Mean relative translations in 3D (mm) |
Max Rel Motion |
Maximum relative motion (mm) |
Mean Abs Motion |
Mean absolute motion in 3D (mm) |
Max Abs Motion |
Maximum absolute motion in 3D (mm) |
Movements (>.1mm) |
Number of relative translations in 3D > .1mm |
Movements (>.5mm) |
Number of relative translations in 3D > .5mm |
Files
The Files pane contains the most commonly requested files. Clicking on any of these files will display that file in the browser
File |
Description |
|---|---|
SNR Image |
BOLD signal SNR image, axiale |
Mean Image |
BOLD signal mean image, axial |
StDev Image |
BOLD signal standard deviation image, axial |
Mask Image |
Masked image |
Mean Slice Image |
BOLD signal mean slice intensity plot |
Motion Data |
Motion (translations and rotations) plot |
Slope Image |
BOLD signal slope image, axial |
Auto QC Report |
Automated QC report |
Slice Report |
Individual slice QC report |
Tabs
To the right of the left pane left pane you’ll find a tab container.
Images
The Images tab displays a zoomed out view of the SNR, Mean, Standard
Deviation, Slope, MEan Slice Intensity, Motion, and Mask images
Clicking on any of these images will display a larger version of the image
Automated QC
The Automated QC tab displays a complete list of BOLDQC metrics.
Manual QC
The Manual QC tab contains a form allowing a quality control
technician to record additional observations, comments, and assign
a final PASS, WARN, or FAIL grade to the scan
All Stored Files
The All Stored Files tab contains a list of every file stored by BOLDQC
Note
Clicking on a file within the All Stored Files tab will download the file.
File |
Description |
|---|---|
|
Automated QC report |
|
Mask snapshot image |
|
Mask NIFTI |
|
Mean snapshot image |
|
Mean NIFTI |
|
Mean slice intensity data |
|
Mean slice intensity plot |
|
Motion plot |
|
Slice report |
|
Slope snapshot image |
|
Slope NIFTI |
|
SNR snapshot image |
|
SNR NIFTI |
|
Standard deviation snapshot image |
|
Standard deviation image |