Mayo Clinic Adult Lifespan Template and Atlases News

MCALT 1.4 released

Christopher Schwarz — Wed, 06 May 2020 12:35:21 GMT

MCALT 1.4 is now released! The included source code 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. There are also some small changes to the MCALT_Lobar atlas.

MCALT version 1.3 Release

Christopher Schwarz — Mon, 24 Sep 2018 1:29:55 GMT

MCALT version 1.3 is released! 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 version 1.2 Release

Christopher Schwarz — Fri, 27 Jul 2018 2:29:02 GMT

MCALT version 1.2 is released!
The new features in this release are:
* 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.

Visit MCALT at AAIC!

Christopher Schwarz — Mon, 23 Jul 2018 2:29:27 GMT

The MCALT authors will be presenting a poster this week at AAIC 2018 in Chicago, detailing the new/upcoming release that includes MCALT segmentation functions. Please visit poster IC-P-189 on Saturday, or P3-382 on Tuesday, to learn about the segmentation methods and ask any questions. Hope to see you there!

MCALT v1.1 Release

Christopher Schwarz — Tue, 05 Sep 2017 1:47:02 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