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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 || (Preprocessing) Process steps 1.1 -1.6 (see below) || || -bedp || (Bedpost) Process step 2 || || -path || (Pathway Reconstruction/Tractography) Process step 3 || === Processing Stages === ==== prep ==== 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 || ==== bedp ==== 2. Stick and ball model fitting with bedpost (Cluster highly recommended for this step) ==== path ==== 3. Pathway reconstruction - Perform tractography for a single subject == Other Arguments (Optional) == || -log <file> || unique log file instead of scripts/trac-all.log || || -noappendlog || overwrite old log files instead of appending || || -cmd <file> || unique cmd file instead of scripts/trac-all.cmd || || -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 || |
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 |
(Preprocessing) Process steps 1.1 -1.6 (see below) |
-bedp |
(Bedpost) Process step 2 |
-path |
(Pathway Reconstruction/Tractography) Process step 3 |
Processing Stages
prep
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 |
bedp
2. Stick and ball model fitting with bedpost (Cluster highly recommended for this step)
path
3. Pathway reconstruction - Perform tractography for a single subject
Other Arguments (Optional)
-log <file> |
unique log file instead of scripts/trac-all.log |
-noappendlog |
overwrite old log files instead of appending |
-cmd <file> |
unique cmd file instead of scripts/trac-all.cmd |
-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 |