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

Stick and ball model fitting with bedpost (Cluster highly recommended for this step)

Path

Pathway reconstruction

-  ⇤ ← Revision 7 as of 2011-02-22 16:44:01 → 
  Size: 659
  Editor: PritiSrinivasan
  Comment:
+   ← Revision 10 as of 2011-02-22 17:33:18 → ⇥
  Size: 2396
  Editor: PritiSrinivasan
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 13:
-== Arguments ==
=== Required Arguments ===
+= Arguments =
== Required Arguments ==
-Line 19:
+Line 18:
-=== Optional Arguments ===
+== Optional Arguments ==
|| -c dmrirc || Configuration File to set analysis options ||
 Line 21:
-|| -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