Mayo Clinic Adult Lifespan Template and Atlases Releases

mcalt 1.5

cgschwarz@www.nitrc.org (Christopher Schwarz) — Tue, 29 Apr 2025 20:53:00 GMT

1.5: 2025/04/29 * Add src/MCALT_PET_spm12_segment.m: Allows computing regional PET SUVR values  consistently with processes in the ADIR Lab at Mayo Clinic * Add atlas/MCALT_TauTemporalMeta_4D.nii: Atlas of the "Tau Temporal Meta"  ROIs, exactly as they were defined and used in Jack et al. papers. * Update: MCALT_v1.5/src/MCALT_Atlas_csv.m now supports "4D" atlases, like  TauTemporalMeta_4D

RS fMRI ROIs and Connectivity Maps 1.0

cgschwarz@www.nitrc.org (Christopher Schwarz) — Fri, 08 Oct 2021 19:14:00 GMT

Mayo Clinic resting-state fMRI ROIs and independent component analysis (ICA) based connectivity maps to study macro-scale functional networks

The Mayo Clinic resting-state fMRI ROIs and independent component analysis (ICA) based connectivity maps were constructed and made publicly available for fMRI analyses in aging and Alzheimer's disease population studies. The first set of ROIs consist in 68 binary masks forming various large-scale intrinsic connectivity networks identified by resting-state fMRI in a sample of healthy older subjects from the Mayo Clinic Study of Aging (MCSA) (Jones et al., 2012). The independent component analysis (ICA) based connectivity maps include both a high and low dimensional decomposition. The high dimensional decomposition contains subnetworks of the default mode network (DMN) (anterior dorsal DMN; anterior ventral DMN; ventral DMN; posterior DMN) that can be utilized to compute the Network Failure Quotient (NFQ), a robust connectivity-based biomarker of macro-scale network failure in Alzheimer's disease (Wiepert et al., 2017).
Full citations:
Jones, D. T., Vemuri, P., Murphy, M. C., Gunter, J. L., Senjem, M. L., Machulda, M. M., ... & Jack Jr, C. R. (2012). Non-stationarity in the "resting brain's" modular architecture. PloS one, 7(6), e39731.
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0039731
Wiepert, D. A., Lowe, V. J., Knopman, D. S., Boeve, B. F., Graff-Radford, J., Petersen, R. C., ... & Jones, D. T. (2017). A robust biomarker of large-scale network failure in Alzheimer's disease. Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring, 6, 152-161.
https://www.sciencedirect.com/science/article/pii/S2352872917300040

MNI_to_MCALT_ANTs_parameters 1.0

cgschwarz@www.nitrc.org (Christopher Schwarz) — Tue, 12 Nov 2019 16:22:00 GMT

ANTs parameter files for transforming between MNI152 and MCALT spaces

mcalt 1.4

cgschwarz@www.nitrc.org (Christopher Schwarz) — Sun, 12 Apr 2020 17:53:00 GMT

1.4: 2020/04/12
* The provided source code (/src directory; MCALT_spm12_segment.m) has new functionality to transform atlases to the input image space using ANTs and calculate per-region GM/tissue volumes and TIV as .csv files. With these additions, this function now re-implements the complete SPM12 T1-weighted processing pipeline used in Dr. Jack's Aging and Dementia Research Lab at Mayo Clinic. Output volumes are not exactly identical but can be directly compared with those computed in-house.
* The MCALT_Lobar atlas has been updated to fill in the posterior "tendrils" of the ventricles, to improve the rate at which tissue in this region may be captured by the atlas.

mcalt 1.3

cgschwarz@www.nitrc.org (Christopher Schwarz) — Wed, 19 Sep 2018 18:16:00 GMT

This release adds three new files to MCALT: 1) a 0.5mm T1-weighted template image; 2) a mask of voxels inside the cranial vault, i.e. the TIV; 3) a segmentation mask designed to remove misclassified adjacent regions of gray-matter-isointense dura from medial temporal lobe (MTL) segmentations.

* ./MCALT_T1_05mm.nii
A higher-resolution (0.5mm) version of MCALT space. This is not the version on which all MCALT atlases were drawn and defined (MCALT_T1.nii). We created this version later, intended primarily for visualizations. It is possible to use this 0.5mm version for atlas propagation, but this has not been rigorously tested. To create this image, the same 202 (~1mm T1-weighted) MRI as in the standard MCALT template were coregistered using buildTemplateParallel.sh from the ANTs package, using a copy of MCALT_T1.nii up-sampled to 0.5mm as a rigid reference target. A single warp (masked to prioritize matching brain voxels) was then calculated between the generated 0.5mm template image and the standard (1.5mm) MCALT_T1.nii. This final warp improved the voxel-wise correspondence between the template versions, thus making it possible to consider this new image to be in the same voxel "space" as MCALT, rather than a new and incompatible template space. All 202 scans were warped via the transforms generated by buildTemplateParallel concatenated with the final warp across templates, then averaged, to create the final MCALT_T1_05mm.nii

* ./MCALT_TIVmask.nii
A mask of MCALT voxels that exist inside the cranial vault, i.e. the total intracranial volume.

* ./atlas/MCALT_MTL_nogo.nii
MCALT_MTL_nogo is a mask designed primarily to remove misclassified adjacent regions of gray-matter-isointense dura from medial temporal lobe (MTL) segmentations. It contains non-brain voxels, proximal to the medial temporal regions, that SPM12 segmentations can sometimes misclassify as brain despite their being labelled as non-brain in our MCALT_tpm. For better segmentation accuracy, we recommend that this mask be applied after segmentation to set any contained voxels as non-GM and non-WM. We typically apply this mask to improve segmentation results in native space. It may also be reasonable to apply this mask to segmentations in template space, but we have not tested it for that use.

mcalt 1.2

cgschwarz@www.nitrc.org (Christopher Schwarz) — Sat, 21 Jul 2018 14:00:00 GMT

This release adds:
* A mask of MCALT voxels that contain primarily brain tissue (gray matter or white matter).
* Matlab source code to perform SPM12 unified segmentation (tissue-class probabilities, bias correction, and normalization to MCALT space) using MCALT tissue priors and our modified segmentation method/settings that are optimized for older adults age 30+. Regional gray matter volumes measured using this segmentation method have larger AUROC values than standard SPM12 pipelines when comparing between matched groups of amyloid-positive cognitively-impaired and amyloid-negative cognitively-unimpaired subjects. See the source code comments and MCALT_Segmentation_Poster.pdf for more information.

mcalt 1.1

cgschwarz@www.nitrc.org (Christopher Schwarz) — Thu, 24 Aug 2017 20:41:00 GMT

This release adds two new atlases defined in MCALT space:
1) MCALT_GlobalPiB, which is used to define amyloid-positivity from amyloid PET scans
2) MCALT_pathologyAtlas, which is used for correlation of imaging and pathologic findings. This atlas has been previously described in: http://onlinelibrary.wiley.com/doi/10.1111/jon.12341/full

mcalt 1.0

cgschwarz@www.nitrc.org (Christopher Schwarz) — Sat, 15 Jul 2017 7:00:00 GMT

Initial release