trac-all
Index
Contents
Name
trac-all : Performs reconstruction of white matter pathways using an atlas of underlying anatomy
Usage
trac-all |
-[Directive] -c <Configuration File> (Using Configuration File to set analysis options) |
trac-all |
-[Directive] -subject subjectname -i dicomfile |
Arguments
Required Arguments
-subject subjid |
the subject data upon which to operate (If not specified in the Configuration File) |
-[Directive] |
one or more directives (see next) |
Optional Arguments
-c dmrirc |
Configuration File to set analysis options |
Fully-Automated Directive
-all |
do everything, including preprocessing, bedpostx and pathway reconstruction |
Manual-Intervention Workflow Directives
-prep |
Process steps 1.1 -1.6 (see below) |
-bedp |
Process step 2 |
-path |
Process step 3 |
Processing Stages
==== Preprocessing ===
- 1.1 Image corrections - Eddy current correction with eddy_correct, B0 field map correction with
- epidewarp.fsl.
-corr
to do this step (Default)
-nocorr
to skip this step
- 1.2 Intra-Subject Registration - Diffusion-to-T1 registration with flirt and/or bbregister.
-intra
to do this step (Default)
-nointra
to skip this step
-inter
to do this step (Default)
-nointer
to skip this step
1.4 White-matter, cortical and whole-brain masks - Generate masks of the white matter and cortex from FreeSurfer outputs,
-masks
to do this step (Default)
-nomasks
to skip this step
- 1.5 Tensor fit - Tensor model fitting on DWIs.
-tensor
to do this step (Default)
-notensor
to skip this step
-prior
to do this step (Default)
-noprior
to skip this step
Bedpost
- Stick and ball model fitting with bedpost (Cluster highly recommended for this step)
Path
- Pathway reconstruction