trac-all Index

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)

For NMR-Center-Users Only

trac-all

-[Directive] -subject subjectname -i dicomfile

For Non-MGH Acquisitions - Please supply the bvals and bvecs in the Configuration File. To see the format of the bvals and bvecs accepted by trac-all, refer to this page

Arguments

Required Arguments

-s subjid

the subject data upon which to operate (If not specified in the Configuration File)

-i DWI file

the full path of the raw Diffusion weighted MR images

-[Directive]

one or more directives (see next)

Optional Arguments

-c dmrirc

Configuration File to set analysis options

Here is how you set up a Configuration File to run Tracula

Clustered Workflow Directives

-prep

(Preprocessing) Process steps 1.1 -1.6 (see below)

-bedp

(Bedpost) Process step 2

-path

(Pathway Reconstruction/Tractography) Process step 3

Processing Stages/Stepwise Directives

(Detailed Explanation for each of these steps is given below) 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

This step performs the following sub-steps:

trac-all -<no>corr -c dmrirc

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

This step performs the following sub-steps:

trac-all -<no>intra -c dmrirc

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

This step performs the following sub-steps: (You can register to either MNI template or CVS template or both. This option can be set in the configuration file) For MNI template

For CVS template

trac-all -<no>inter -c dmrirc

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

trac-all -<no>masks -c dmrirc

1.5 Tensor fit - Tensor model fitting on DWIs.

-tensor

to do this step (Default)

-notensor

to skip this step

This step performs the following sub-steps:

trac-all -<no>tensor -c dmrirc

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

trac-all -<no>prior -c dmrirc

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

trac-all -bedp -c dmrirc

3. Pathway reconstruction - Perform tractography for a single subject

trac-all -path -c dmrirc

Status and Log files (Optional)

-log file

default is $SUBJECTS_DIR/<your_subjectid>/scripts/trac-all.log

-cmd file

default is $SUBJECTS_DIR/<your_subjectid>/scripts/trac-all.cmd

-noappendlog

start new log and status files instead of appending

Other Arguments (Optional)

-no-isrunning

do not check whether dubjects are currently being processed

-sd subjectsdir

specify subjects dir

-umask umask

set unix file permission mask (default 002)

-grp groupid

check that current group is alpha groupid

-allowcoredump

set coredump limit to unlimited

-debug

generate much more output

dontrun

do everything but execute each command

-onlyversions

print version of each binary and exit

-version

print version of this script and exit

-help

print full contents of help

Output Directories and Files

Running trac-all creates a new directory named <subjid> (if subject id is specified through the commandline) or <subjlist(i)> (if a subjectlist is specified through the configuration file, where i is index of the subject that is currently being processed)

Outputs from trac-all -corr

Note: The list below does not include outputs from B0 inhomogenity correction This creates three directories under the <subjid> directory (i) dlabel/diff (ii) dmri (iii) scripts

Outputs from trac-all -intra

Note: <regtype>: flt (FLIRT) / bbr (BBREGISTER) This step creates a folder <subjid>/dmri/xfms

Outputs from trac-all -inter

The following outputs get created if registering to an MNI template.

The following outputs get created if registering to CVS template. This step creates a symbolic link <subjid>/dmri/xfms/cvs to the folder $SUBJECTS_DIR/cvs where the freesurfer recons are present. It also creates a folder under $SUBJECTS_DIR/cvs for each of the image used as a CVS template. We recommend using the template given with the freesurfer distribution (cvs_avg35) although you can use your own atlas.

Outputs from trac-all -masks