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| ==== 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~ || 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
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
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 |
2. Stick and ball model fitting with bedpost (Cluster highly recommended for this step) 3. Pathway reconstruction - Perform tractography for a single subject
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 |
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~ || 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