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'''Index''' <<TableOfContents>> |
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= 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 || 1.3 Inter-Subject Registration - T1-to-template registration using MNI and/or CVS templates. || -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, whole-brain masks from T1 and DWIs. || -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 || 1.6 Pathway priors from atlas to T1 - Combine training data and subject's own data to generate pathway priors. || -prior || to do this step (Default) || || -noprior || to skip this step || ==== Bedpost ==== 2. Stick and ball model fitting with bedpost (Cluster highly recommended for this step) ==== Path ==== 3. Pathway reconstruction |
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 |
1.3 Inter-Subject Registration - T1-to-template registration using MNI and/or CVS templates.
-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, whole-brain masks from T1 and DWIs.
-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 |
1.6 Pathway priors from atlas to T1 - Combine training data and subject's own data to generate pathway priors.
-prior |
to do this step (Default) |
-noprior |
to skip this step |
Bedpost
2. Stick and ball model fitting with bedpost (Cluster highly recommended for this step)
Path
3. Pathway reconstruction