Neocortical and subcortial feature post-processing with z-brains
relies heavily on micapipe,
an openly available, multimodal MRI pre-processing pipeline. The sections below outline the minimal pre-processing that should be perfomed with
micapipe
prior to running z-brains
, for each modality available in your dataset.
The Brain Imaging Data Structure (BIDS)
The Brain Imaging Data Structure (BIDS) is a widely used directory and file naming convention in brain imaging. To run micapipe
, and subsequently z-brains
, your raw data needs to be conform to BIDS standards.
Core to the z-brains
architecture are the computation and resampling of neocortical surface segmentations via micapipe
. This allows for smoothing and normalization of available features across participants.
Generation of these features rely on the structural processing of micapipe
Key outputs of these modules for z-brains
are:
Outputs | Description |
---|---|
Processed T1w image | A new space, nativepro , is created and used for all downstream processing and cross-modality registrations. This image is generated from the intensity non-uniformity-corrected, rescaled raw T1w image. If multiple T1w acquisitions are available, their are co-registered and average prior to intensity correction steps. |
Neocortical surface reconstructions | Neocortical surfaces are initially generated by FreeSurfer/FastSurfer (called through micapipe ), and resampled to symmetric, standard templates (fs-LR) aligned to the participant's nativepro space. |
Neocortical thickness | Thickness estimates are computed by FreeSurfer/FastSurfer, and mapped to resampled fs-LR surface templates |
Subcortical structure volume | Subcortical volumes are provided by FreeSurfer/FastSurfer (called through micapipe ) |
Subcortical structure segmentation | Subcortical structures are segmented using FSL FIRST, and the resulting parcellation is used to sample image intensities for relevant features. |
Generation of these features rely on the FLAIR processing of micapipe
Key outputs of this module for z-brains
are:
Outputs | Description |
---|---|
Processed FLAIR image | Pre-processed FLAIR image (bias correction, intensity clamping and rescaling, and normalization to gray/white matter interface values) co-registered to nativepro space. This image is used for intensity sampling in z-brains subcortical and hippocampal processing modules. |
Processed FLAIR intensities mapped to neocortical surface | Neocortical surfaces are initially generated by FreeSurfer/FastSurfer (called through micapipe ), and resampled to symmetric, standard templates (fs-LR) aligned to the participant's nativepro space. |
Generation of these features rely on the Microstructural profile covariance module of micapipe
Key outputs of this module for z-brains
are:
Outputs | Description |
---|---|
Processed T1 map volume | The qT1 image co-registered to nativepro space. This image is used for intensity sampling in z-brains subcortical and hippocampal processing modules. |
T1 relaxation times mapped to neocortical surfaces | Neocortical surfaces are initially generated by FreeSurfer/FastSurfer (called through micapipe ), and resampled to symmetric, standard templates (fs-LR) aligned to the participant's nativepro space. |
Generation of these features rely on the diffusion-weighted imaging module of micapipe
Key outputs of this module for z-brains
are:
Outputs | Description |
---|---|
Processed MD volume | The MD image co-registered to nativepro space. This image is used for intensity sampling in z-brains subcortical and hippocampal processing modules. |
Processed FA volume | The FA image co-registered to nativepro space. This image is used for intensity sampling in z-brains subcortical and hippocampal processing modules. |
MD and FA values mapped to neocortical surfaces | Neocortical surfaces are initially generated by FreeSurfer/FastSurfer (called through micapipe ), and resampled to symmetric, standard templates (fs-LR) aligned to the participant's nativepro space. |