XNAT user documentation

Tagging your scans

For AnatQC to discover T1w and vNav scans to process, you need to add notes to those scans in XNAT. You can add notes using the Edit button located within the Actions box on the MR Session report page

Type	Example series	Note
T1w	`ABCD_T1w_MPR_vNav`	`#T1w_001, #T1w_002, ..., #T1w_N`
vNav	`ABCD_T1w_MPR_vNav_setter`	`#T1w_move_001, #T1w_move_002, ..., #T1w_move_N`

The image below displays an MR Session report page with populated notes

Note

Note that if a T1w scan has a corresponding vNav scan, they should be assigned matching numbers. For example, #T1w_move_001 would correspond to #T1w_001.

Running the pipeline

To run the AnatQC pipeline, use the Run Containers > anatqc-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 several configurable settings. Continue reading for a description of each setting

run

This should be set to the integer value of the scan you want to process. If there’s a corresponding move scan, that scan will also be processed

T1w scan	run
`#T1w_001`	1
`#T1w_002`	2
`#T1w_999`	999

subtasks

Under most circumstances you’ll want to leave this field set to its default value

morph mriqc vnav

fslicense

This field should be set to a base64 encoded FreeSurfer license. If you have a license file on a Linux or macOS machine, you can use the openssl command

openssl base64 < license.txt

or you can use the base64 command, if that utility is installed

base64 license.txt

Understanding the report page

The following section will break down each section of the AnatQC 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
Date Processed	Processing date
T1w scan	T1-weighted scan used
vNav scan	vNav setter scan used (if present)

QC Metrics

The QC Metrics pane displays quality control metrics computed over the entire volume

Metric	From	Description
SNR Tot	MRIQC	Signal-to-noise ratio
EFC	MRIQC	Entropy Focus Criterion
FWHM Avg	MRIQC	FWHM of spatial distribution of voxel intensities
GM SNR	MRIQC	Gray matter signal-to-noise ratio
WM SNR	FreeSurfer	White matter signal-to-noise ratio
CNR	FreeSurfer	Contrast-to-noise ratio

Hemispheres

The Hemispheres pane displays quality control metrics computed over each hemisphere

Metric	From	Description
Euler Holes	FreeSurfer	Estimate of the number of surface defects
CNR	FreeSurfer	Global contrast-to-noise ratio
G/W CNR	FreeSurfer	Gray and white matter contrast-to-noise ratio
G/CSF CNR	FreeSurfer	Gray matter and cerebrospinal fluid contrast-to-noise ratio

vNav

The vNav pane displays vNav specific quality control metrics, but only if a vNav scan was processed

Metric	Description
Settings	Minimum and maximum number of navigators allowed
Motion Score RMS	Root mean square of motion scores
Motion Score Max	Maximum motion score
vNav Acq	Total number of navigators collected
Failed	vNav failure detected

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
T1w axial	T1-weighted image, axial plane
Surfaces axial	FreeSurfer surface boundaries, axial plane
Segmentation axial	FreeSurfer segmentations, axial plane
Brainmask axial	FreeSurfer brain mask, axial plane
vNav Motion Scores RMS	vNav motion scores RMS plot
Cortical Laterality	Cortical region volume laterality plot
Subcortical Laterality	Subcortical region volume laterality plot
MRIQC Report	MRIQC HTML report

Tabs

To the right of the left pane you’ll find a tab container. The following section explains the contents of each tab.

Images

The Images tab displays a zoomed out view of the T1-weighted image, FreeSurfer surface boundaries, FreeSurfer segmentations, and vNav RMS motion scores

Clicking on an image within the Images tab will display a larger version of that image in the browser

Note

AnatQC automatically crops and centers each brain slice for improved visibility. For this reason, slices will often appear larger than their native size.

MRIQC Report tab

The MRIQC Report tab displays the complete MRIQC HTML report

MRIQC IQMs

The MRIQC IQMs tab displays all of the MRIQC Image Quality Metrics. These metrics can also be found within the MRIQC HTML Report

All Stored Files

The All Stored Files tab contains a list of every file stored by AnatQC

Note

Clicking on a file within the All Stored Files tab will download that file.

File	Description
`*_AQC_T1w_axial.png`	T1-weighted image, axial plane
`*_AQC_aseg_axial.png`	FreeSurfer segmentations, axial plane
`*_AQC_brainmask_axial.png`	FreeSurfer brain mask image, axial plane
`*_AQC_surface_axial.png`	FreeSurfer surface boundaries, axial plane
`*_AQC_aparc_laterality.png`	FreeSurfer parcellation laterality plot
`*_AQC_aseg_laterality.png`	FreeSurfer segmentation laterality plot
`*_AQC_mriqc.html`	MRIQC HTML report
`*_AQC_freesurfer.tar.gz`	FreeSurfer results
`*_AQC_vNav_Motion.json`	vNav processing output
`*_AQC_vNavMotionScoresMax.png`	vNav motion max plot
`*_AQC_vNavMotionScoresRMS.png`	vNav motion RMS plot