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) |
For NMR-Center-Users Only
Do not submit trac-all as a command in the cluster but run it on the command line. It will submit each subject listed in the Configuration File file as a seperate job to the cluster.
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:
- Convert the input Diffusion Dicoms to NIFTI (This is skipped if a NIFTI file is given as the input)
- Change orientation of the input Diffusion images to match FSL's orientation
B0 inhomogenity correction (This is done using fsl's fieldmap based EPI unwarping tool epdiewarp.fsl/epdidewarp.fsl. In order to do this step, B0 field map magnitude dicoms should be specified in the Configuration file)
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 |
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 |
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 |
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
SUBJECT_DIR/SUBJECT_NAME
dlabel
anat
anat_brain_mask.nii.gz |
anat_brain_mask-vent.nii.gz |
aparc+aseg.nii.gz |
cortex+2mm+bs.nii.gz |
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