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| * 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) * |
* <Optional> 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) * Eddy Current / Simple head motion Correction (Eddy currents within the gradient coils induce distortions which can be corrected by a simple affine registration to a reference volume (low-b volume). This step is done using fsl's eddy_correct) * Create a low-b Diffusion brain mask {{{ |
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This step performs the following sub-steps: * Change orientation of the T1 anatomical image to match FSL's orientation * Compute forward and inverse transformation matrices between the original T1 and re-oriented T1. * Compute forward and inverse transformation matrices between T1(Original and re-oriented) and low-b Diffusion image using FLIRT and/or BBREGISTER |
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
<Optional> B0 inhomogenity correction (This is done using fsl's fieldmap based EPI unwarping tool epdidewarp.fsl. In order to do this step, B0 field map magnitude dicoms should be specified in the Configuration file)
- Eddy Current / Simple head motion Correction (Eddy currents within the gradient coils induce distortions which can be corrected by a simple affine registration to a reference volume (low-b volume). This step is done using fsl's eddy_correct)
- Create a low-b Diffusion brain mask
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:
- Change orientation of the T1 anatomical image to match FSL's orientation
- Compute forward and inverse transformation matrices between the original T1 and re-oriented T1.
- Compute forward and inverse transformation matrices between T1(Original and re-oriented) and low-b Diffusion image using FLIRT and/or BBREGISTER
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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