As a researcher, I want to segment T1-weighted anatomical MRI images in order to
(1) quantify brain volume (as well as GM, WM & CSF volume),
(2) derive an anatomical brainmask,
(3) derive a mask for cortical/sub-cortical structures, and/or,
(3) use segmentation image for subsequent analysis (i.e., anatomically-constrained diffusion tractography).
Notes
This process should include 3 sub-processes:
(1) FreeSurfer/FastSurfer recon-all
(2) 5-tissue-type generation5ttgen hsvs
(3) Desikan-Killiany (DK) parcellation
*using mrtrix3 commands in Pydra
Acceptance Criteria
Given a T1-weighted anatomical MRI image, when this pipeline is executed, the following outputs should be generated:
[x] standard FreeSurfer/FastSurfer outputs directory
Metadata
Epic: #17 Feature: #79 Feature Release: Required knowledge: mid-level
Description
As a researcher, I want to segment T1-weighted anatomical MRI images in order to (1) quantify brain volume (as well as GM, WM & CSF volume), (2) derive an anatomical brainmask, (3) derive a mask for cortical/sub-cortical structures, and/or, (3) use segmentation image for subsequent analysis (i.e., anatomically-constrained diffusion tractography).
Notes
This process should include 3 sub-processes: (1) FreeSurfer/FastSurfer
recon-all(2) 5-tissue-type generation5ttgen hsvs(3) Desikan-Killiany (DK) parcellation*using mrtrix3 commands in Pydra
Acceptance Criteria
Given a T1-weighted anatomical MRI image, when this pipeline is executed, the following outputs should be generated: