The results for CIVET are created in the directory targetdir, as specified in the command-line options. The file References.txt in this directory gives a list of references to cite in your paper. These references describe the various algorithms and modules used in your CIVET run. Please acknowlege the work of these researchers in your publications using CIVET.

CIVET organizes the results for each subject in targetdir/id where id is the identifier of the subject. Note that the presence of some files may be activated by your choice of parameters.

Listing of Output Folders / Files

  • native : images in native space
    • prefix_id_t1.mnc : original t1 image, without direction cosines, z,y,x internal ordering, regular spacing, mnc2
    • prefix_id_t1_nuc.mnc : t1 image partially corrected for non-uniformities
If t2/pd used as input:
  • prefix_id_t2.mnc : original t2 image, without direction cosines, z,y,x internal ordering, regular spacing, mnc2
  • prefix_id_t2_nuc.mnc : t2 image partially corrected for non-uniformities
  • prefix_id_pd.mnc : original pd image, without direction cosines, z,y,x internal ordering, regular spacing, mnc2
  • prefix_id_pd_nuc.mnc : pd image partially corrected for non-uniformities
  • final : images in stereotaxic space
    • prefix_id_t1_tal.mnc : original t1 image transformed in stereotaxic space
    • prefix_id_t1_final.mnc : original t1 image transformed in stereotaxic space, fully corrected for non-uniformities (with mask)
If t2/pd used as input:
  • prefix_id_t2_tal.mnc : original t2 image transformed in stereotaxic space
  • prefix_id_t2_final.mnc : original t2 image transformed in stereotaxic space, fully corrected for non-uniformities (with mask)
  • prefix_id_pd_tal.mnc : original pd image transformed in stereotaxic space
  • prefix_id_pd_final.mnc : original pd image transformed in stereotaxic space, fully corrected for non-uniformities (with mask)
  • transforms/linear : linear transformations
    • prefix_id_t1_tal.xfm : linear transformation from t1 native to stereotaxic space
    • prefix_id_t1_tal_to_6.xfm : linear transformation from stereotaxic space to 6 parameter space
    • prefix_id_t1_tal_to_7.xfm : linear transformation from stereotaxic space to 7 parameter space
If t2/pd used as input:
  • prefix_id_t2pd_t1.xfm : 6-param linear transformation from t2/pd to t1
  • prefix_id_t2pd_tal.xfm : linear transformation from t2/pd to stereotaxic space
  • transforms/nonlinear : non-linear transformations
    • prefix_id_nlfit_It.xfm : non-linear transformation from linear stereotaxic space to stereotaxic space
    • prefix_id_nlfit_It_grid_0.mnc : deformation field for non-linear transformation
  • transforms/surfreg : surface transformations
    • prefix_id_left_surfmap.sm
      prefix_id_right_surfmap.sm : surface maps for left/right hemispheres to surface model
  • mask : brain masks in stereotaxic space
    • prefix_id_skull_mask.mnc : brain mask of cerebrum + cerebellum and brain stem
    • prefix_id_brain_mask.mnc : brain mask without cerebellum and brain stem
  • classify : classified image in stereotaxic space
    • prefix_id_cls_clean.mnc : masked discrete tissue classification
    • prefix_id_cls_volumes.dat : total volume of tissue types in native space (masked, containing cerebrum only, no cerebellum or brainstem, in mm3: 1 = all CSF; 2 = all GM, subcortical and cortical; 3 = all WM)
    • prefix_id_pve_disc.mnc : pure and mixed tissue classes (0 = BG; 1 = CSF; 2 = GM; 3 = WM; 4 = sub-cortical GM; 5 = mixed CSF-GM; 6 = mixed GM-WM; 7 = mixed BG-CSF; 8 = mixed sub-cortical GM-WM; 9 = mixed sub-cortical GM-GM)
    • prefix_id_pve_exactcsf.mnc : partial volume estimates for csf
    • prefix_id_pve_exactgm.mnc : partial volume estimates for gray matter
    • prefix_id_pve_exactwm.mnc : partial volume estimates for white matter
    • prefix_id_pve_classify.mnc : final discrete tissue classification after correction for partial volumes
  • surfaces : surfaces and related files in stereotaxic space
    • prefix_id_white_surface.obj :
      prefix_id_white_surface_left_81920.obj :
      prefix_id_white_surface_right_81920.obj : final white matter surfaces after t1-gradient correction (if hires option selected, there will additionally be versions with the suffix *_327680.obj)
    • prefix_id_white_surface_rsl.obj :
      prefix_id_white_surface_rsl_left_81920.obj :
      prefix_id_white_surface_rsl_right_81920.obj : final white matter surfaces, resampled to MNI ICBM152 surface model or other selected model (if hires option selected, there will only be versions with the suffix *_327680.obj)
    • prefix_id_gray_surface.obj :
      prefix_id_gray_surface_left_81920.obj :
      prefix_id_gray_surface_right_81920.obj : final gray matter (pial) surfaces (if hires option selected, there will additionally be versions with the suffix *_327680.obj)
    • prefix_id_gray_surface_rsl.obj :
      prefix_id_gray_surface_rsl_left_81920.obj :
      prefix_id_gray_surface_rsl_right_81920.obj : final gray matter surfaces, resampled to MNI ICBM152 surface model or other selected model (if hires option selected, there will only be versions with the suffix *_327680.obj)
    • prefix_id_mid_surface.obj :
      prefix_id_mid_surface_left_81920.obj :
      prefix_id_mid_surface_right_81920.obj : final mid surfaces, halfway between white and gray (if hires option selected, there will only be versions with the suffix *_327680.obj)
    • prefix_id_mid_surface_rsl.obj :
      prefix_id_mid_surface_rsl_left_81920.obj :
      prefix_id_mid_surface_rsl_right_81920.obj : final mid surfaces, resampled to MNI ICBM152 surface model or other selected model (if hires option selected, there will only be versions with the suffix *_327680.obj)
    • prefix_id_native_pos_rsl_asym_full.txt :
      prefix_id_native_pos_rsl_asym_hemi.txt : asymmetry maps for position on mid resampled surfaces, whole brain or by hemisphere
    • prefix_id_mid_surface_rsl_left_native_area_40mm.txt :
      prefix_id_mid_surface_rsl_right_native_area_40mm.txt : vertex-based elementary areas on resampled hemispheric surfaces (default = 40,962 vertices per hemi, hires = 163,842 vertices per hemi)
    • prefix_id_surface_rsl_left_native_volume_40mm.txt :
      prefix_id_surface_rsl_right_native_volume_40mm.txt : vertex-based elementary volumes on resampled hemispheric surfaces (default = 40,962 vertices per hemi, hires = 163,842 vertices per hemi)
    • prefix_id_gi.dat :
      prefix_id_gi_left.dat :
      prefix_id_gi_right.dat : gyrification index for gray, white, mid surfaces
    • prefix_id_lobe_thickness_tlink_30mm_left.dat:
      prefix_id_lobe_thickness_tlink_30mm_right.dat: regional average cortical thickness (collapsed across vertices per region) at this (30mm) fwhm; depends on parcellation selected (basic lobar, AAL, or DKT40)
    • prefix_id_lobe_volumes_40mm_left.dat:
      prefix_id_lobe_volumes_40mm_right.dat: regional average volumes (collapsed across vertices per region) at this (40mm) fwhm; depends on parcellation selected (basic lobar, AAL, or DKT40)
    • prefix_id_lobe_areas_40mm_left.dat:
      prefix_id_lobe_areas_40mm_right.dat: regional average areas (collapsed across vertices per region) at this (40mm) fwhm of the resampled mid surface, in native space; depends on parcellation selected (basic lobar, AAL, or DKT40)
    • prefix_id_lobe_native_cortex_area_left.dat:
      prefix_id_lobe_native_cortex_area_right.dat: regional average areas (collapsed across vertices per region) of the resampled gray surface, in native space; depends on parcellation selected (basic lobar, AAL, or DKT40)
  • thickness : cortical thickness maps
    • prefix_id_cerebral_volume.dat : total volume of cortex in native space (masked, containing cerebrum only, in mm3: 1 = CSF outside pial surface only (without ventricles); 2 = cortical GM only (no subcortical); 3 = WM + subcortical gray + filled-in ventricles)
    • prefix_id_native_rms_tlink_30mm.txt :
      prefix_id_native_rms_tlink_30mm_left.txt :
      prefix_id_native_rms_tlink_30mm_right.txt : native cortical thickness, blurred at this (30mm) fwhm (default = 40,962 vertices per hemi, hires = 163,842 vertices per hemi)
    • prefix_id_native_rms_rsl_tlink_30mm.txt :
      prefix_id_native_rms_rsl_tlink_30mm_left.txt :
      prefix_id_native_rms_rsl_tlink_30mm_right.txt : native cortical thickness, resampled to MNI ICBM152 surface model or other selected model, blurred this (30mm) fwhm (default = 40,962 vertices per hemi, hires = 163,842 vertices per hemi)
    • prefix_id_native_rms_rsl_tlink_30mm_asym.txt :
      prefix_id_native_rms_rsl_tlink_30mm_asym_hemi.txt : asymmetry maps for cortical thickness, resampled to MNI ICBM152 surface model or other selected model (resampled left-right, default = 40,962 vertices per hemi, hires = 163,842 vertices per hemi)
If -mean-curvature option selected:
  • prefix_id_native_mc_30mm_gray.txt :
    prefix_id_native_mc_30mm_gray_left.txt :
    prefix_id_native_mc_30mm_gray_right.txt : mean surface curvature for GM surface, blurred at this (30mm) fwhm (default = 40,962 vertices per hemi, hires = 163,842 vertices per hemi)
  • prefix_id_native_mc_30mm_mid.txt :
    prefix_id_native_mc_30mm_mid_left.txt :
    prefix_id_native_mc_30mm_mid_right.txt : mean surface curvature for mid surface, blurred at this (30mm) fwhm (default = 40,962 vertices per hemi, hires = 163,842 vertices per hemi)
  • prefix_id_native_mc_30mm_white.txt :
    prefix_id_native_mc_30mm_white_left.txt :
    prefix_id_native_mc_30mm_white_right.txt : mean surface curvature for WM surface, blurred at this (30mm) fwhm (default = 40,962 vertices per hemi, hires = 163,842 vertices per hemi)
  • prefix_id_native_mc_rsl_30mm_gray.txt :
    prefix_id_native_mc_rsl_30mm_gray_left.txt :
    prefix_id_native_mc_rsl_30mm_gray_right.txt : mean surface curvature, resampled to MNI ICBM152 surface model or other selected model, blurred at this (30mm) fwhm (default = 40,962 vertices per hemi, hires = 163,842 vertices per hemi)
  • prefix_id_native_mc_rsl_30mm_mid.txt :
    prefix_id_native_mc_rsl_30mm_mid_left.txt :
    prefix_id_native_mc_rsl_30mm_mid_right.txt : mean surface curvature, resampled to MNI ICBM152 surface model or other selected model, blurred at this (30mm) fwhm (default = 40,962 vertices per hemi, hires = 163,842 vertices per hemi)
  • prefix_id_native_mc_rsl_30mm_white.txt :
    prefix_id_native_mc_rsl_30mm_white_left.txt :
    prefix_id_native_mc_rsl_30mm_white_right.txt : mean surface curvature, resampled to MNI ICBM152 surface model or other selected model, blurred at this (30mm) fwhm (default = 40,962 vertices per hemi, hires = 163,842 vertices per hemi)
  • VBM : non-modulated VBM maps in stereotaxic space (if -VBM selected)
    • prefix_id_smooth_8mm_csf.mnc :
      prefix_id_smooth_8mm_gm.mnc :
      prefix_id_smooth_8mm_wm.mnc : VBM maps for CSF, gray matter, or white matter, blurred at 8mm
If -VBM-symmetry option selected:
  • prefix_id_smooth_8mm_csf_sym.mnc :
    prefix_id_smooth_8mm_gm_sym.mnc :
    prefix_id_smooth_8mm_wm_sym.mnc : right/left differences of blurred VBM maps for CSF, gray matter, or white matter
  • segment : ANIMAL segmentation (if -animal selected)
    • prefix_id_animal_labels.mnc : ANIMAL segmentation, unmasked
    • prefix_id_animal_labels_masked.mnc : ANIMAL segmentation, masked
    • prefix_id_lobes.dat : regional segmented volumes, in native space, mm3 (See bottom of page here for ANIMAL label list)
  • temp : temporary working files (not documented)
  • verify : quality control images
    • prefix_id_atlas.png : quality control image for surface registration and lobar segmentation
    • prefix_id_clasp.png : quality control image for surface extraction
    • prefix_id_laplace.png : quality control image for gray surface expansion
    • prefix_id_surfsurf.png : quality control image for surface-surface intersections
    • prefix_id_verify.png : quality control image for registration and classification
    • prefix_id_classify_qc.txt : classified tissue percentages
    • prefix_id_surface_qc.txt : error for white and gray surfaces
    • prefix_id_civet_qc.txt : list of values of processing variables for populating the QC table
  • logs : execution log and status for stages
    • id.stage_name.log : log of commands for stage
    • id.stage_name.lock : lock file (indicates if a subject is being processed)
    • id.stage_name.running : status file (indicates if a stage is ready to run or is running)
    • id.stage_name.failed : status file (indicates if a stage has failed)
    • id.stage_name.finished : status file (indicates if a stage has completed successfully)
    • id.options : options and settings used to process subject

Understanding CIVET errors

The log files are useful to determine the completion status of CIVET. After completion, one should check for the presence of .failed and .running files. A leftover .running means that the CIVET run is incomplete, likely due to some unexpected interruption (power failure?). A .failed file means that a stage has failed. In such a case, examine the corresponding .log file for that stage to try to understand the cause of the error. Note that there are usually leftover .running files for the unfinished stages after a failure. Sometimes, you may also have to manually erase the .lock files after a crash if their presence prevents you from restarting CIVET. Common errors are:

  • t1 image in non-standard orientation (often after conversion from NIfTI to minc)
  • t1 image not centered within the field of view causing the failure of the clean_native_scan stage. If your image originates from DICOM, make sure to use the -usecoordinates option in the dcm2mnc converter. If you are converting from NIfTI, make sure that you have used the latest version of the nii2mnc converter.
  • empty brain mask causing tissue classification to be undefined
  • incorrect linear registration to stereotaxic space
  • incomplete cortical surfaces due to self-intersections of the white marching-cubes surface following surface registration (usually nothing to do except check for the presence of blood vessels, and re-run with option -mask-blood-vessels)

Whenever such an error occurs, it is helpful to view the MR input and processed images in a minc viewer (BIC tools register, Display, or BrainBrowser) to understand the source of the error.

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