Differences between revisions 25 and 32 (spanning 7 versions)
⇤ ← Revision 25 as of 2011-05-13 11:29:12 →
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Editor: PritiSrinivasan
Comment:
← Revision 32 as of 2011-05-13 13:50:21 → ⇥
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Editor: PritiSrinivasan
Comment:
Deletions are marked like this. Additions are marked like this.
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||trac-all ||-[Directive] -c <Configuration File> (Using Configuration File to set analysis options) || ||trac-all ||-[Directive] -c <[[FsTutorial/Tracula|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 [[FsTutorial/Tracula|Configuration File]] file as a seperate job to the cluster.''
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'''For Non-MGH Acquisitions''' - Please supply the bvals and bvecs in the [[FsTutorial/Tracula|Configuration File]]. To see the format of the bvals and bvecs accepted by trac-all, refer to this [[FsTutorial/Tracula|page]]
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||-subject subjid ||the subject data upon which to operate (If not specified in the Configuration File) || ||-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 ||
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Here is how you set up a [[FsTutorial/Tracula|Configuration File]] to run Tracula
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== Fully-Automated Directive ==
||-all ||do everything, including preprocessing, bedpostx and pathway reconstruction ||


== Manual-Intervention Workflow Directives ==		 == Clustered Workflow Directives ==
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=== Processing Stages ===
1.1 Image corrections - Eddy current correction with eddy_correct, B0 field map correction with epidewarp.fsl.		 === 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
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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)
 *
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trac-all -<no>corr -c dmrirc
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trac-all -<no>intra -c dmrirc
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trac-all -<no>inter -c dmrirc
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trac-all -<no>masks -c dmrirc
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trac-all -<no>tensor -c dmrirc
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trac-all -<no>prior -c dmrirc
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trac-all -bedp -c dmrirc
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trac-all -path -c dmrirc
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||cortex+2mm.nii.gz ||
||cortex.nii.gz ||
||notventricles.nii.gz ||
||White-Matter.nii.gz ||
||White-Matter++.nii.gz ||


==== anatorig ====
||anat_brain_mask.nii.gz ||
||anat_brain_mask-vent.nii.gz ||
||aparc+aseg.nii.gz ||
||Brain-Stem.nii.gz ||
||cortex+2mm+bs.nii.gz ||
||cortex_2mm.nii.gz ||
||cortex.nii.gz ||
||lowb_brain_mask.bbr.nii.gz ||
||lowb_brain_mask.flt.nii.gz ||
||notventricles.nii.gz ||
||White-Matter.nii.gz ||
||White-Matter++.nii.gz ||


==== cvs ====
||anat_brain_mask.nii.gz ||
||anat_brain_mask-vent.nii.gz ||
||aparc+aseg.nii.gz ||
||cortex+2mm+bs.nii.gz ||
||cortex+2mm.nii.gz ||
||cortex.nii.gz ||
||lowb_brain_mask.bbr.nii.gz ||
||lowb_brain_mask.flt.nii.gz ||
||notventricles.nii.gz ||
||White-Matter.nii.gz ||
||White-Matter++.nii.gz ||


==== diff ====
||anat_brain_mask.bbr.nii.gz ||
||anat_brain_mask.flt.nii.gz ||
||anat_brain_mask-vent.bbr.nii.gz ||
||anat_brain_mask-vent.flt.nii.gz ||
||aparc+aseg.bbr.nii.gz ||
||aparc+aseg.flt.nii.gz ||
||cortex+2mm.bbr.nii.gz ||
||cortex+2mm.flt.nii.gz ||
||cortex+2mm+bs.bbr.nii.gz ||
||cortex+2mm+bs.flt.nii.gz ||
||cortex.bbr.nii.gz ||
||cortex.flt.nii.gz ||
||lowb_brain_mask.nii.gz ||
||notventricles.bbr.nii.gz ||
||notventricles.bbr.nii.gz ||
||White-Matter.bbr.nii.gz ||
||White-Matter.flt.nii.gz ||
||White-Matter++.bbr.nii.gz ||
||White-Matter++.flt.nii.gz ||


==== mni ====
||anat_brain_mask.nii.gz ||
||anat_brain_mask-vent.nii.gz ||
||aparc+aseg.nii.gz ||
||cortex+2mm+bs.nii.gz ||
||cortex+2mm.nii.gz ||
||cortex.nii.gz ||
||lowb_brain_mask.bbr.nii.gz ||
||lowb_brain_mask.flt.nii.gz ||
||notventricles.nii.gz ||
||White-Matter.nii.gz ||
||White-Matter++.nii.gz ||


=== dmri ===
||brain_anat_mni.nii.gz ||
||brain_anat.nii.gz ||
||brain_anat_orig.nii.gz ||
||bvals ||
||bvecs ||
||bvecs.norot ||
||data.nii.gz *Same as dwi.nii.gz* ||
||dcminfo.dat ||
||dtifit_FA.nii.gz ||
||dtifit_L1.nii.gz ||
||dtifit_L2.nii.gz ||
||dtifit_L3.nii.gz ||
||dtifit_MD.nii.gz ||
||dtifit_MO.nii.gz ||
||dtifit_S0.nii.gz ||
||dtifit_V1.nii.gz ||
||dtifit_V2.nii.gz ||
||dtifit_V3.nii.gz ||
||dwi.ecclog ||
||dwi.nii.gz ||
||dwi_orig_flip.nii.gz ||
||dwi_orig.mghdti.bvals ||
||dwi_orig.mghdti.bvecs ||
||dwi_orig.nii.gz ||
||dwi_snr.txt ||
||lowb_brain_anat.flt.nii.gz ||
||lowb_brain.nii.gz ||
||lowb.nii.gz ||
||nodif_brain_mask.nii.gz *Same as Subject#/dlabel/diff/anat_brain_mask.bbr.nii.gz* ||


==== xfms ====
||anat2anatorig.dat ||
||anat2anatorig.mat ||
||anat2diff.bbr.mat ||
||anat2diff.flt.mat ||
||anat2mni.mat ||
||anatorig2anat.mat ||
||anatorig2diff.bbr.dat ||
||anatorig2diff.bbr.dat.log ||
||anatorig2diff.bbr.dat.mincost ||
||anatorig2diff.bbr.dat.param ||
||anatorig2diff.bbr.dat.sum ||
||anatorig2diff.bbr.mat ||
||anatorig2diff.flt.mat ||
||anatorig2mni.mat ||


==== cvs ====
||combined_elreg_afteraseg-norm-aseg.mgz ||
||combined_elreg_afteraseg-norm.tm3d ||
||combined_elreg_aseg_norm.mgz ||
||combined_elreg_aseg.tm3d ||
||el_reg_toavg35rerun_aseg.mgz ||
||el_reg_toavg35rerun.mgz ||
||el_reg_toavg35rerun.tm3d ||
||lh.dbg_surf.pial ||
||lh.dbg_surf.white ||
||lh.resample.aparc.annot ||
||lh.resample.pial ||
||lh.resample.white ||
||nlalign-afteraseg-norm.m3z ||
||nlalign-afteraseg-norm.mgz ||
||nlalign-aseg.m3z ||
||nlalign-aseg.mgz ||
||rh.dbg_surf.pial ||
||rh.dbg_surf.white ||
||rh.resample.aparc.annot ||
||rh.resample.pial ||
||rh.resample.white ||
||trace_el_reg_toavg35rerun_M02100024.txt ||
||transform.txt ||
||diff2anat.bbr.mat ||
||diff2anat.flt.mat ||
||diff2anatorig.bbr.mat ||
||diff2anatorig.flt.mat ||
||diff2mni.bbr.mat ||
||diff2mni.flt.mat ||
||mni2anat.mat ||
||mni2anatorig.mat ||
||mni2diff.bbr.mat ||
||mni2diff.flt.mat ||


=== dmri.bedpostx ===
||bvals ||
||bvecs ||
||cancel ||
||commands.txt ||
||cputime ||
||dyads1_dispersion.nii.gz ||
||dyads1.nii.gz ||
||dyads2_dispersion.nii.gz ||
||dyads2.nii.gz ||


==== logs ====
||joblist ||
||log0000 ||
||log0001 ||
||log0002 ||
||log0003 ||
||log0004 ||
||log0005 ||
||log0006 ||
||log0007 ||
||log0008 ||
||log0009 ||
||log0010 ||
||log0011 ||
||log0012 ||
||log0013 ||
||log0014 ||
||log0015 ||
||log0016 ||
||log0017 ||
||log0018 ||
||log0019 ||
||log0020 ||
||log0021 ||
||log0022 ||
||log0023 ||
||log0024 ||
||log0025 ||
||log0026 ||
||log0027 ||
||log0028 ||
||log0029 ||
||log0030 ||
||log0031 ||
||log0032 ||
||log0033 ||
||log0034 ||
||log0035 ||
||log0036 ||
||log0037 ||
||log0038 ||
||log0039 ||
||log0040 ||
||log0041 ||
||log0042 ||
||log0043 ||
||log0044 ||
||log0045 ||
||log0046 ||
||log0047 ||
||log0048 ||
||log0049 ||
||log0050 ||
||log0051 ||
||log0052 ||
||log0053 ||
||log0054 ||
||log0055 ||
||log0056 ||
||log0057 ||
||log0058 ||
||log0059 ||
||log0060 ||
||log0061 ||
||log0062 ||
||log0063 ||
||pid_8911 ||
||mean_dsamples.nii.gz ||
||mean_f1samples.nii.gz ||
||mean_f2samples.nii.gz ||
||mean_ph1samples.nii.gz ||
||mean_ph2samples.nii.gz ||
||mean_th1samples.nii.gz ||
||mean_th2samples.nii.gz ||
||merged_f1samples.nii.gz ||
||merged_f2samples.nii.gz ||
||merged_ph1samples.nii.gz ||
||merged_ph2samples.nii.gz ||
||merged_th1samples.nii.gz ||
||merged_th2samples.nii.gz ||
||monitor ||
||nodif_brain_mask.nii.gz ||




==== xfms ====
||eye.mat ||


=== scripts ===
||build-stamp.txt ||
||csurfdir ||
||dmrirc.local ||
||dmrirc.local.orig ||
||trac-all.cmd ||
||trac-all.local-copy ||
||trac-all.log ||
||trac-preproc.done ||
||trac-preproc.local-copy ||		 |

trac-all

Index

Contents

  1. Name
  2. Usage
  3. Arguments
    1. Required Arguments
    2. Optional Arguments
    3. Clustered Workflow Directives
      1. Processing Stages/Stepwise Directives
    4. Status and Log files (Optional)
    5. Other Arguments (Optional)
  4. Output Directories and Files
    1. SUBJECT_DIR/SUBJECT_NAME
      1. dlabel
        1. anat

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

|

trac-all (last edited 2021-12-08 16:06:06 by AnastasiaYendiki)