7 Voxel-Based Morphometry
This starter kit walk through the voxel-based morphometry outputs generated by the Computational Anatomy Toolbox (CAT12).
7.1 Starting Project
7.1.1 Locate data
On TACC, the neuroimaging data are stored underneath the releases. For example, data release v2.#.# is underneath
pre-surgery/mrisThe morphometry measures are underneath derivatives/cat12.
7.1.2 Extract data
Data for each participant is stored in a sub-directory
$ ls -d derivatives/cat12/sub* | head
derivatives/cat12/sub-10003
derivatives/cat12/sub-10005
derivatives/cat12/sub-10008
derivatives/cat12/sub-10009
derivatives/cat12/sub-10010
derivatives/cat12/sub-10011
derivatives/cat12/sub-10013
derivatives/cat12/sub-10014
derivatives/cat12/sub-10015
derivatives/cat12/sub-10017For example:
$ tree derivatives/cat12/sub-10003
derivatives/cat12/sub-10003
└── ses-V1
├── label
│ ├── catROI_sub-10003_ses-V1_T1w.mat
│ └── catROI_sub-10003_ses-V1_T1w.xml
├── mri
│ ├── misub-10003_ses-V1_T1w.nii
│ ├── msub-10003_ses-V1_T1w.nii
│ ├── mwp1sub-10003_ses-V1_T1w.nii
│ ├── mwp2sub-10003_ses-V1_T1w.nii
│ ├── mwp3sub-10003_ses-V1_T1w.nii
│ ├── p0sub-10003_ses-V1_T1w.nii
│ ├── p1sub-10003_ses-V1_T1w.nii
│ ├── p2sub-10003_ses-V1_T1w.nii
│ ├── p3sub-10003_ses-V1_T1w.nii
│ ├── wmisub-10003_ses-V1_T1w.nii
│ ├── wmsub-10003_ses-V1_T1w.nii
│ ├── wp0sub-10003_ses-V1_T1w.nii
│ ├── wp1sub-10003_ses-V1_T1w.nii
│ ├── wp2sub-10003_ses-V1_T1w.nii
│ ├── wp3sub-10003_ses-V1_T1w.nii
│ └── y_sub-10003_ses-V1_T1w.nii
├── report
│ ├── catlog_sub-10003_ses-V1_T1w.txt
│ ├── cat_sub-10003_ses-V1_T1w.mat
│ └── cat_sub-10003_ses-V1_T1w.xml
└── surf
├── lh.central.sub-10003_ses-V1_T1w.gii
├── lh.pbt.sub-10003_ses-V1_T1w
├── lh.pial.sub-10003_ses-V1_T1w.gii
├── lh.sphere.reg.sub-10003_ses-V1_T1w.gii
├── lh.sphere.sub-10003_ses-V1_T1w.gii
├── lh.thickness.sub-10003_ses-V1_T1w
├── lh.white.sub-10003_ses-V1_T1w.gii
├── rh.central.sub-10003_ses-V1_T1w.gii
├── rh.pbt.sub-10003_ses-V1_T1w
├── rh.pial.sub-10003_ses-V1_T1w.gii
├── rh.sphere.reg.sub-10003_ses-V1_T1w.gii
├── rh.sphere.sub-10003_ses-V1_T1w.gii
├── rh.thickness.sub-10003_ses-V1_T1w
└── rh.white.sub-10003_ses-V1_T1w.gii
5 directories, 35 filesAdditionally, there is a table of “cluster volumes”, which contains information relevant to A2CPS primary and secondary biomarkers.
$ ls derivatives/cat12/cluster*
derivatives/cat12/cluster_volumes.json derivatives/cat12/cluster_volumes.tsv
$ head derivatives/cat12/cluster_volumes.tsv
sub ses mri atlas cluster volume
10703 V1 wp1sub-10703_ses-V1_T1w tpl-MNI152NLin2009cAsym_atlas-smallwood_dseg 0 1998.106000518892
10703 V1 wp1sub-10703_ses-V1_T1w tpl-MNI152NLin2009cAsym_atlas-smallwood_dseg 1 2294.6824886463583
10703 V1 mwp1sub-10703_ses-V1_T1w tpl-MNI152NLin2009cAsym_atlas-smallwood_dseg 0 1219.69091796875
10703 V1 mwp1sub-10703_ses-V1_T1w tpl-MNI152NLin2009cAsym_atlas-smallwood_dseg 1 1443.6837158203125
10753 V1 mwp1sub-10753_ses-V1_T1w tpl-MNI152NLin2009cAsym_atlas-smallwood_dseg 0 1673.0926513671875
10753 V1 mwp1sub-10753_ses-V1_T1w tpl-MNI152NLin2009cAsym_atlas-smallwood_dseg 1 1950.593505859375
10753 V1 wp1sub-10753_ses-V1_T1w tpl-MNI152NLin2009cAsym_atlas-smallwood_dseg 0 2353.910433325509
10753 V1 wp1sub-10753_ses-V1_T1w tpl-MNI152NLin2009cAsym_atlas-smallwood_dseg 1 2952.608998143696
10040 V1 mwp1sub-10040_ses-V1_T1w tpl-MNI152NLin2009cAsym_atlas-smallwood_dseg 0 1499.8414306640625The json file contains a data dictionary, with links to confluence pages providing detailed information about each of the atlases.
{
"sub": {
"LongName": "Subject",
"Description": "Study Participant, BIDS Subject ID",
"TermURL": "https://bids-specification.readthedocs.io/en/v1.9.0/appendices/entities.html#sub"
},
"ses": {
"LongName": "Session",
"Description": "Visit, Protocol, BIDS Session ID",
"Levels": {
"V1": "baseline_visit",
"V3": "3mo_postop"
},
"TermURL": "https://bids-specification.readthedocs.io/en/v1.9.0/appendices/entities.html#ses"
},
"mri": {
"LongName": "MRI Filename",
"Description": "Product of CAT12 in which volumes were calculated",
"TermURL": "https://neuro-jena.github.io/cat12-help/#naming"
},
"atlas": {
"LongName": "Atlas of Clusters",
"Description": "Source file in which clusters are defined",
"Levels": {
"tpl-MNI152NLin2009cAsym_atlas-smallwood_dseg": "https://a2cps.atlassian.net/wiki/external/NjFmMGViNjA1OGI4NGIxNWJlMjk0ZmM5ODcyNDhhODc",
"tpl-MNI152NLin2009cAsym_atlas-henn_desc-controlspatientgmtfce05_dseg": "https://doi.org/10.1097/j.pain.0000000000002681, Table 4"
}
},
"cluster": {
"LongName": "Cluster Number",
"Description": "ID of cluster as reported by FSL. May not match ID in source paper."
},
"volume": {
"LongName": "Cluster Volume",
"Description": "Volume of cluster_id from atlas_id in mri_id calculated as number of voxels times voxel volume."
}
}7.2 Considerations While Working on the Project
7.2.1 Variability Across Scanners
Many MRI biomarkers exhibit variability across the scanners, which may confound some analyses. For an up-to-date assessment of the issue and overview of current thinking, please see Confluence.
7.2.2 Data Quality
As with any MRI derivative, all pipeline derivatives have been included. This means that products were included regardless of their quality, and so some products may have been generated from images that are known to have poor quality—rated “red”, or incomparable. For details on the ratings and how to exclude them, see Appendix A. Additionally, extensive QC has not yet been performed on the derivatives themselves, and so there may be cases where pipelines produced atypical outputs. For an overview of planned checks, see Confluence.
7.2.3 CAT12 Configuration
For details on CAT12’s methods see their documentation. CAT12 (12.9, r2582) was run with nearly the default configurations, changing only parameters that cause a few additional outputs to be saved. For the full batch script, see GitHub.
7.2.4 CAT12 Image Quality Ratings
Part of the Raw MRI data quality ratings are derived from an “Image Quality Rating” that is provided by CAT12. The ratings were pulled from the xml document in the reports subfolder. For example
$ grep -P "<IQR>|\(IQR\)" sub-10003/ses-V1/report/cat_sub-10003_ses-V1_T1w.xml
<IQR>1.85445149536238</IQR>
<item>Image Quality Rating (IQR): 86.46% (B)</item>The version of the IQR reported as a percentage is equal to \(105 - 10*IQR\).
Note that CAT12 typically generates a PDF with an overview of processing and image quality. There is an ongoing issue with CAT12 that prevented the PDFs from being generated for Release 2.0.0. For details, see the associated issue on the CAT12 GitHub Repo.
7.2.5 Citations
The methods driving CAT12 are based on extensive research. If you use these results, please be sure to cite the relevant papers outlined here: https://neuro-jena.github.io/cat/index.html#About.
In publications or presentations including data from A2CPS, please include the following statement as attribution:
Data were provided [in part] by the A2CPS Consortium funded by the National Institutes of Health (NIH) Common Fund, which is managed by the Office of the Director (OD)/ Office of Strategic Coordination (OSC). Consortium components and their associated funding sources include Clinical Coordinating Center (U24NS112873), Data Integration and Resource Center (U54DA049110), Omics Data Generation Centers (U54DA049116, U54DA049115, U54DA049113), Multi-site Clinical Center 1 (MCC1) (UM1NS112874), and Multi-site Clinical Center 2 (MCC2) (UM1NS118922).