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 Outputs

  • 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
    • 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)
    • 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_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
    • prefix_id_cortex.obj: surface representation of brain_mask
  • 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 (masked) in native space (in mm3) (1=CSF; 2=GM; 3=WM)
    • prefix_id_pve_disc.mnc : pure and mixed tissue classes
    • 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 in stereotaxic space
    • prefix_id_white_surface.obj :
      prefix_id_white_surface_left_81920.obj :
      prefix_id_white_surface_right_81920.obj : white matter surfaces
    • prefix_id_white_surface_calibrated.obj :
      prefix_id_white_surface_left_calibrated_81920.obj :
      prefix_id_white_surface_right_calibrated_81920.obj : final white matter surfaces after t1-gradient correction
    • prefix_id_white_surface_rsl_calibrated.obj :
      prefix_id_white_surface_rsl_left_calibrated_81920.obj :
      prefix_id_white_surface_rsl_right_calibrated_81920.obj : resampled calibrated white surfaces
    • prefix_id_gray_surface.obj :
      prefix_id_gray_surface_left_81920.obj :
      prefix_id_gray_surface_right_81920.obj : final gray matter (pial) surfaces
    • prefix_id_gray_surface_rsl.obj :
      prefix_id_gray_surface_rsl_left_81920.obj :
      prefix_id_gray_surface_rsl_right_81920.obj : resampled gray matter surfaces
    • prefix_id_mid_surface.obj :
      prefix_id_mid_surface_left_81920.obj :
      prefix_id_mid_surface_right_81920.obj : final mid surfaces (between white and gray)
    • prefix_id_mid_surface_rsl.obj :
      prefix_id_mid_surface_rsl_left_81920.obj :
      prefix_id_mid_surface_rsl_right_81920.obj : resampled mid surfaces
    • prefix_id_left_dataterm.vv :
      prefix_id_right_dataterm.vv : sulcal depth potential map for surface registration
    • 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
    • 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
    • prefix_id_gi.dat :
      prefix_id_gi_left.dat :
      prefix_id_gi_right.dat : gyrification index for white, mid, gray surfaces
    • prefix_id_lobe_thickness_tlink_30mm_left.dat:
      prefix_id_lobe_thickness_tlink_30mm_right.dat: regional average vertex-based cortical thickness at this fwhm
    • prefix_id_lobe_areas_40mm_left.dat:
      prefix_id_lobe_areas_40mm_right.dat: regional average vertex-based areas at this fwhm
    • prefix_id_lobe_volumes_40mm_left.dat:
      prefix_id_lobe_volumes_40mm_right.dat: regional average vertex-based volumes at this fwhm
  • thickness : cortical thickness maps
    • prefix_id_cerebral_volume.dat : volume of cortex in native space (label 2 only)
    • prefix_id_native_mc_20mm.txt :
      prefix_id_native_mc_20mm_left.txt :
      prefix_id_native_mc_20mm_right.txt : mean surface curvature, blurred at 20mm
    • prefix_id_native_mc_rsl_20mm_left.txt :
      prefix_id_native_mc_rsl_20mm_right.txt : resampled mean surface curvature, blurred at 20mm
    • prefix_id_native_rms_tlink_20mm.txt :
      prefix_id_native_rms_tlink_20mm_left.txt :
      prefix_id_native_rms_tlink_20mm_right.txt : native cortical thickness, blurred at 20mm
    • prefix_id_native_rms_rsl_tlink_20mm.txt :
      prefix_id_native_rms_rsl_tlink_20mm_left.txt :
      prefix_id_native_rms_rsl_tlink_20mm_right.txt : resampled native cortical thickness, blurred at 20mm
    • prefix_id_native_rms_rsl_tlink_20mm_asym.txt : asymmetry maps for cortical thickness
      prefix_id_native_rms_rsl_tlink_20mm_asym_hemi.txt : asymmetry maps for cortical thickness (resampled left-right)
  • VBM : VBM maps in stereotaxic space
    • 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
    • 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 (not available in this version)
  • temp : temporary working file (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
  • 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)
  • empty brain mask causing tissue classification to be undefined
  • incorrect linear registration to stereotaxic space

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


CIVET Home