Differences between revisions 24 and 34 (spanning 10 versions)

trac-all

Index

Contents

Name
Usage
Arguments
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
<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

This step performs the following sub-steps: (You can register to either MNI template or CVS template or both)

Compute forward and inverse transformations between T1(Original and re-oriented) and MNI atlas
Combine the low-b to T1 transformation (from the intra subject registration step) with the above transformation to get low-b to MNI/MNI to low-b transformations
Compute

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

-  ⇤ ← Revision 24 as of 2011-03-18 17:14:15 → 
  Size: 9034
  Editor: PritiSrinivasan
  Comment:
+   ← Revision 34 as of 2011-05-13 17:15:06 → ⇥
  Size: 5767
  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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+Line 18:
+'''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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+Line 22:
-||-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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+Line 25:
-Line 22:
+Line 29:
+Here is how you set up a [[FsTutorial/Tracula|Configuration File]] to run Tracula
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+Line 31:
-== Fully-Automated Directive ==
||-all ||do everything, including preprocessing, bedpostx and pathway reconstruction ||


== Manual-Intervention Workflow Directives ==
+== Clustered Workflow Directives ==
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+Line 37:
-=== 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
-Line 38:
+Line 44:
+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 [[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 
{{{
trac-all -<no>corr -c dmrirc
}}}
-Line 45:
+Line 57:
+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
}}}
-Line 52:
+Line 68:
+This step performs the following sub-steps: (You can register to either MNI template or CVS template or both)
 * Compute forward and inverse transformations between T1(Original and re-oriented) and MNI atlas
 * Combine the low-b to T1 transformation (from the intra subject registration step) with the above transformation to get low-b to MNI/MNI to low-b transformations
 * Compute 
{{{
trac-all -<no>inter -c dmrirc
}}}
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+Line 79:
+trac-all -<no>masks -c dmrirc
-Line 66:
+Line 85:
+trac-all -<no>tensor -c dmrirc
-Line 73:
+Line 91:
+trac-all -<no>prior -c dmrirc
-Line 74:
+Line 93:
+. Stick and ball model fitting with bedpost (Cluster highly recommended for this step)
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+Line 95:
+trac-all -bedp -c dmrirc
-Line 76:
+Line 97:
-. Stick and ball model fitting with bedpost (Cluster highly recommended for this step) 3. Pathway reconstruction - Perform tractography for a single subject
+. Pathway reconstruction - Perform tractography for a single subject

trac-all -path -c dmrirc
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+Line 121:
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+Line 129:
-||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 ||
+|