Differences between revisions 21 and 23 (spanning 2 versions)
⇤ ← Revision 21 as of 2011-02-22 18:40:18 →
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Editor: PritiSrinivasan
Comment:
← Revision 23 as of 2011-02-23 12:12:35 → ⇥
Size: 9034
Editor: PritiSrinivasan
Comment:
Deletions are marked like this. Additions are marked like this.
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'''Index'''
<<TableOfContents>>		 '''Index''' <<TableOfContents>>
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|| trac-all || -[Directive] -c <Configuration File> (Using Configuration File to set analysis options) ||
|| trac-all || -[Directive] -subject subjectname -i dicomfile ||		 ||trac-all ||-[Directive] -c <Configuration File> (Using Configuration File to set analysis options) ||
||trac-all ||-[Directive] -subject subjectname -i dicomfile ||
Line 15: Line 15:
|| -subject subjid || the subject data upon which to operate (If not specified in the Configuration File) ||
|| -[Directive] || one or more directives (see next) ||		 ||-subject subjid ||the subject data upon which to operate (If not specified in the Configuration File) ||
||-[Directive] ||one or more directives (see next) ||
Line 19: Line 20:
|| -c dmrirc || Configuration File to set analysis options || ||-c dmrirc ||Configuration File to set analysis options ||
Line 22: Line 24:
|| -all || do everything, including preprocessing, bedpostx and pathway reconstruction || ||-all ||do everything, including preprocessing, bedpostx and pathway reconstruction ||
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|| -prep || (Preprocessing) Process steps 1.1 -1.6 (see below) ||
|| -bedp || (Bedpost) Process step 2 ||
|| -path || (Pathway Reconstruction/Tractography) Process step 3 ||		 ||-prep ||(Preprocessing) Process steps 1.1 -1.6 (see below) ||
||-bedp ||(Bedpost) Process step 2 ||
||-path ||(Pathway Reconstruction/Tractography) Process step 3 ||
Line 31: Line 35:
|| -corr || to do this step (Default) ||
|| -nocorr || to skip this step ||		 ||-corr ||to do this step (Default) ||
||-nocorr ||to skip this step ||
Line 34: Line 42:
|| -intra || to do this step (Default) ||
|| -nointra || to skip this step ||		 ||-intra ||to do this step (Default) ||
||-nointra ||to skip this step ||
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|| -inter || to do this step (Default) ||
|| -nointer || to skip this step ||		 ||-inter ||to do this step (Default) ||
||-nointer ||to skip this step ||
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|| -masks || to do this step (Default) ||
|| -nomasks || to skip this step ||		 ||-masks ||to do this step (Default) ||
||-nomasks ||to skip this step ||
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|| -tensor || to do this step (Default) ||
|| -notensor || to skip this step ||		 ||-tensor ||to do this step (Default) ||
||-notensor ||to skip this step ||
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|| -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		 ||-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
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|| -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 ||		 ||-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 ||
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|| -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 ||		 ||-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 ||
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|| 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 ||		 ||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 ||
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|| 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 ||		 ||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 ||
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|| 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 ||		 ||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 ||
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|| 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 ||		 ||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 ||
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|| 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 ||		 ||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 ||
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|| 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* ||		 ||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* ||
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|| 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 ||		 ||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 ||
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|| 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 ||		 ||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 ||
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|| bvals ||
|| bvecs ||
|| cancel ||
|| commands.txt ||
|| cputime ||
|| dyads1_dispersion.nii.gz ||
|| dyads1.nii.gz ||
|| dyads2_dispersion.nii.gz ||
|| dyads2.nii.gz ||		 ||bvals ||
||bvecs ||
||cancel ||
||commands.txt ||
||cputime ||
||dyads1_dispersion.nii.gz ||
||dyads1.nii.gz ||
||dyads2_dispersion.nii.gz ||
||dyads2.nii.gz ||
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|| 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 ||		 ||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 ||
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|| eye.mat || ||eye.mat ||
Line 312: Line 365:
|| 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 ||
 		 ||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. Fully-Automated Directive
    4. Manual-Intervention Workflow Directives
      1. Processing Stages
    5. Status and Log files (Optional)
    6. Other Arguments (Optional)
  4. Output Directories and Files
    1. SUBJECT_DIR/SUBJECT_NAME
      1. dlabel
        1. anat
        2. anatorig
        3. cvs
        4. diff
        5. mni
      2. dmri
        1. xfms
        2. cvs
      3. dmri.bedpostx
        1. logs
        2. xfms
      4. scripts

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