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| '''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 [[FsTutorial/Tracula|page]] | |
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| 1.1 Image corrections - Eddy current correction with eddy_correct, B0 field map correction with epidewarp.fsl. | (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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| To do just eddy current correction and B0 field map correction on the images the following command can be used. trac-all -corr -c dmrirc |
This step performs the following steps: 1.1 trac-all -<no>corr -c dmrirc |
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| trac-all -intra -c dmrirc | trac-all -<no>intra -c dmrirc |
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| trac-all -inter -c dmrirc | trac-all -<no>inter -c dmrirc |
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| trac-all -masks -c dmrirc | trac-all -<no>masks -c dmrirc |
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| trac-all -tensor -c dmrirc | trac-all -<no>tensor -c dmrirc |
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| trac-all -prior -c dmrirc | trac-all -<no>prior -c dmrirc |
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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 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 steps:
- 1.1
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 |
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 |