Structural MRI Processing - katielavigne/documentation GitHub Wiki
Several different morphometrics can be extracted from structural magnetic resonance imaging (MRI) data, including volume, cortical thickness, and surface area. Below are instructions for several pipelines used at McGill and the Douglas Research Centre. Many of these pipelines are provided by the CobraLab (PI: Mallar Chakravarty) and the ACELab (PI: Alan Evans) so please consult their documentation as well.
BPIPE PROCESSING
(Pre-)Processing pipeline to convert scans to minc format, correct for intensity non-uniformities, and create brain masks, among other things.
External documentation
CIVET
Surface-based metrics (surface-based volume, cortical thickness, and surface area) are calculated with CIVET through the CBRAIN platform. You may also run CIVET via command line on the Douglas Cerebral Imaging Centre or Compute Canada compute nodes.
External documentation
- CIVET Manual
- CBRAIN User Manual
- CIVET Command Line Instructions (via CobraLab)
MAGeT
Volume-based metrics (for us, this is mainly volume of the hippocampus and its subfields) are calculated using the MAGeTbrain algorithm.
External documentation
Quantitative T1 Sampling
Scripts for computing quantitative T1 (MP2RAGE) values for MAGeT labels and CIVET surfaces.
External documentation