Workbench Command is a set of command-line tools that can be used to perform simple and complex operations within Connectome Workbench.
-add-to-spec-file ADD A FILE TO A SPECIFICATION FILE -annotation-resample RESAMPLE AN ANNOTATION FILE TO DIFFERENT MESHES -backend-average-dense-roi CONNECTOME DB BACKEND COMMAND FOR CIFTI AVERAGE DENSE ROI -backend-average-roi-correlation CONNECTOME DB BACKEND COMMAND FOR CIFTI AVERAGE ROI CORRELATION -border-export-color-table WRITE BORDER NAMES AND COLORS AS TEXT -border-file-export-to-caret5 EXPORT BORDER FILE TO CARET5 FILE FORMAT -border-length REPORT LENGTH OF BORDERS -border-merge MERGE BORDER FILES INTO A NEW FILE -border-resample RESAMPLE A BORDER FILE TO A DIFFERENT MESH -border-to-rois MAKE METRIC ROIS FROM BORDERS -border-to-vertices DRAW BORDERS AS VERTICES IN A METRIC FILE -cifti-all-labels-to-rois MAKE ROIS FROM ALL LABELS IN A CIFTI LABEL MAP -cifti-average AVERAGE CIFTI FILES -cifti-average-dense-roi AVERAGE CIFTI ROWS ACROSS SUBJECTS BY ROI -cifti-average-roi-correlation CORRELATE ROI AVERAGE WITH ALL ROWS THEN AVERAGE ACROSS SUBJECTS -cifti-change-mapping CONVERT TO SCALAR, COPY MAPPING, ETC -cifti-convert DUMP CIFTI MATRIX INTO OTHER FORMATS -cifti-correlation GENERATE CORRELATION OF ROWS IN A CIFTI FILE -cifti-correlation-gradient CORRELATE CIFTI ROWS AND TAKE GRADIENT -cifti-create-dense-from-template CREATE CIFTI WITH MATCHING DENSE MAP -cifti-create-dense-scalar CREATE A CIFTI DENSE SCALAR FILE -cifti-create-dense-timeseries CREATE A CIFTI DENSE TIMESERIES -cifti-create-label CREATE A CIFTI LABEL FILE -cifti-create-parcellated-from-template MATCH PARCELS TO TEMPLATE BY NAME -cifti-create-scalar-series IMPORT SERIES DATA INTO CIFTI -cifti-cross-correlation CORRELATE A CIFTI FILE WITH ANOTHER CIFTI FILE -cifti-dilate DILATE A CIFTI FILE -cifti-erode ERODE A CIFTI FILE -cifti-estimate-fwhm ESTIMATE FWHM SMOOTHNESS OF A CIFTI FILE -cifti-export-dense-mapping WRITE INDEX TO ELEMENT MAPPING AS TEXT -cifti-extrema FIND EXTREMA IN A CIFTI FILE -cifti-false-correlation COMPARE CORRELATION LOCALLY AND ACROSS/THROUGH SULCI/GYRI -cifti-find-clusters FILTER CLUSTERS BY AREA/VOLUME -cifti-gradient TAKE GRADIENT OF A CIFTI FILE -cifti-label-adjacency MAKE ADJACENCY MATRIX OF A CIFTI LABEL FILE -cifti-label-export-table EXPORT LABEL TABLE FROM CIFTI AS TEXT -cifti-label-import MAKE A CIFTI LABEL FILE FROM A CIFTI FILE -cifti-label-modify-keys CHANGE KEY VALUES IN A DLABEL FILE -cifti-label-probability FIND FREQUENCY OF CIFTI LABELS -cifti-label-to-border DRAW BORDERS AROUND CIFTI LABELS -cifti-label-to-roi MAKE A CIFTI LABEL INTO AN ROI -cifti-math EVALUATE EXPRESSION ON CIFTI FILES -cifti-merge MERGE OR SPLIT ON SERIES, SCALAR, OR LABEL DIMENSIONS -cifti-merge-dense MERGE CIFTI FILES ALONG DENSE DIMENSION -cifti-merge-parcels MERGE CIFTI FILES ALONG PARCELS DIMENSION -cifti-pairwise-correlation CORRELATE PAIRED ROWS BETWEEN TWO CIFTI FILES -cifti-palette SET PALETTE ON A CIFTI FILE -cifti-parcel-mapping-to-label CREATE DLABEL FROM PARCELLATED FILE -cifti-parcellate PARCELLATE A CIFTI FILE -cifti-reduce PERFORM REDUCTION OPERATION ON A CIFTI FILE -cifti-reorder REORDER THE PARCELS OR SCALAR/LABEL MAPS IN A CIFTI FILE -cifti-replace-structure REPLACE DATA IN A STRUCTURE IN A CIFTI FILE -cifti-resample RESAMPLE A CIFTI FILE TO A NEW CIFTI SPACE -cifti-resample-dconn-memory USE LOTS OF MEMORY TO RESAMPLE DCONN -cifti-restrict-dense-map EXCLUDE BRAINORDINATES FROM A CIFTI FILE -cifti-roi-average AVERAGE ROWS IN A SINGLE CIFTI FILE -cifti-rois-from-extrema CREATE CIFTI ROI MAPS FROM EXTREMA MAPS -cifti-separate WRITE A CIFTI STRUCTURE AS METRIC, LABEL OR VOLUME -cifti-smoothing SMOOTH A CIFTI FILE -cifti-stats STATISTICS ALONG CIFTI COLUMNS -cifti-transpose TRANSPOSE A CIFTI FILE -cifti-vector-operation DO A VECTOR OPERATION ON CIFTI FILES -cifti-weighted-stats WEIGHTED STATISTICS ALONG CIFTI COLUMNS -class-add-member ADD MEMBER AND GETTER/SETTER TO SOURCE CODE FILES (.h and .cxx) -class-create CREATE CLASS SOURCE CODE FILES (.h and .cxx) -class-create-algorithm CREATE SOURCE CODE CLASS FILES (.h, .cxx) FOR ALGORITHM -class-create-enum CREATE SOURCE CODE CLASS FILES (.h, .cxx) FOR ENUMERATED TYPE -class-create-operation CREATE SOURCE CODE CLASS FILES (.h, .cxx) FOR OPERATION -convert-affine CONVERT AN AFFINE FILE BETWEEN CONVENTIONS -convert-fiber-orientations CONVERT BINGHAM PARAMETER VOLUMES TO FIBER ORIENTATION FILE -convert-matrix4-to-matrix2 GENERATES A MATRIX2 CIFTI FROM MATRIX4 WBSPARSE -convert-matrix4-to-workbench-sparse CONVERT A 3-FILE MATRIX4 TO A WORKBENCH SPARSE FILE -convert-warpfield CONVERT A WARPFIELD BETWEEN CONVENTIONS -create-signed-distance-volume CREATE SIGNED DISTANCE VOLUME FROM SURFACE -estimate-fiber-binghams ESTIMATE FIBER ORIENTATION DISTRIBUTIONS FROM BEDPOSTX SAMPLES -fiber-dot-products COMPUTE DOT PRODUCTS OF FIBER ORIENTATIONS WITH SURFACE NORMALS -file-convert CHANGE VERSION OF FILE FORMAT -file-information LIST INFORMATION ABOUT A FILE'S CONTENT -foci-create CREATE A FOCI FILE -foci-get-projection-vertex GET PROJECTION VERTEX FOR FOCI -foci-list-coords OUTPUT FOCI COORDINATES IN A TEXT FILE -foci-resample PROJECT FOCI TO A DIFFERENT SURFACE -gifti-all-labels-to-rois MAKE ROIS FROM ALL LABELS IN A GIFTI COLUMN -gifti-convert CONVERT A GIFTI FILE TO A DIFFERENT ENCODING -gifti-label-add-prefix ADD PREFIX TO ALL LABEL NAMES IN A GIFTI LABEL FILE -gifti-label-to-roi MAKE A GIFTI LABEL INTO AN ROI METRIC -label-dilate DILATE A LABEL FILE -label-erode ERODE A LABEL FILE -label-export-table EXPORT LABEL TABLE FROM GIFTI AS TEXT -label-mask MASK A LABEL FILE -label-merge MERGE LABEL FILES INTO A NEW FILE -label-modify-keys CHANGE KEY VALUES IN A LABEL FILE -label-probability FIND FREQUENCY OF SURFACE LABELS -label-resample RESAMPLE A LABEL FILE TO A DIFFERENT MESH -label-to-border DRAW BORDERS AROUND LABELS -label-to-volume-mapping MAP LABEL FILE TO VOLUME -metadata-remove-provenance REMOVE PROVENANCE INFORMATION FROM FILE METADATA -metadata-string-replace REPLACE A STRING IN ALL METADATA OF A FILE -metric-convert CONVERT METRIC FILE TO FAKE NIFTI -metric-dilate DILATE A METRIC FILE -metric-erode ERODE A METRIC FILE -metric-estimate-fwhm ESTIMATE FWHM SMOOTHNESS OF A METRIC FILE -metric-extrema FIND EXTREMA IN A METRIC FILE -metric-false-correlation COMPARE CORRELATION LOCALLY AND ACROSS/THROUGH SULCI/GYRI -metric-fill-holes FILL HOLES IN AN ROI METRIC -metric-find-clusters FILTER CLUSTERS BY SURFACE AREA -metric-gradient SURFACE GRADIENT OF A METRIC FILE -metric-label-import IMPORT A GIFTI LABEL FILE FROM A METRIC FILE -metric-mask MASK A METRIC FILE -metric-math EVALUATE EXPRESSION ON METRIC FILES -metric-merge MERGE METRIC FILES INTO A NEW FILE -metric-palette SET THE PALETTE OF A METRIC FILE -metric-reduce PERFORM REDUCTION OPERATION ACROSS METRIC COLUMNS -metric-regression REGRESS SPATIAL MAP OUT OF A METRIC FILE -metric-remove-islands REMOVE ISLANDS FROM AN ROI METRIC -metric-resample RESAMPLE A METRIC FILE TO A DIFFERENT MESH -metric-rois-from-extrema CREATE METRIC ROI MAPS FROM EXTREMA MAPS -metric-rois-to-border DRAW BORDERS AROUND METRIC ROIS -metric-smoothing SMOOTH A METRIC FILE -metric-stats SPATIAL STATISTICS ON A METRIC FILE -metric-tfce DO TFCE ON A METRIC FILE -metric-to-volume-mapping MAP METRIC FILE TO VOLUME -metric-vector-operation DO A VECTOR OPERATION ON METRIC FILES -metric-vector-toward-roi FIND IF VECTORS POINT TOWARD AN ROI -metric-weighted-stats WEIGHTED SPATIAL STATISTICS ON A METRIC FILE -nifti-information DISPLAY INFORMATION ABOUT A NIFTI/CIFTI FILE -probtrackx-dot-convert CONVERT A .DOT FILE FROM PROBTRACKX TO CIFTI -scene-capture-image OFFSCREEN RENDERING OF SCENE TO AN IMAGE FILE -scene-file-merge REARRANGE SCENES INTO A NEW FILE -scene-file-relocate RECREATE SCENE FILE IN NEW LOCATION -scene-file-update UPDATE SCENE FILE -set-map-names SET THE NAME OF ONE OR MORE MAPS IN A FILE -set-structure SET STRUCTURE OF A DATA FILE -signed-distance-to-surface COMPUTE SIGNED DISTANCE FROM ONE SURFACE TO ANOTHER -spec-file-merge MERGE TWO SPEC FILES INTO ONE -spec-file-relocate RECREATE SPEC FILE IN NEW LOCATION -surface-affine-regression REGRESS THE AFFINE TRANSFORM BETWEEN SURFACES ON THE SAME MESH -surface-apply-affine APPLY AFFINE TRANSFORM TO SURFACE FILE -surface-apply-warpfield APPLY WARPFIELD TO SURFACE FILE -surface-average AVERAGE SURFACE FILES TOGETHER -surface-closest-vertex FIND CLOSEST SURFACE VERTEX TO COORDINATES -surface-coordinates-to-metric MAKE METRIC FILE OF SURFACE COORDINATES -surface-cortex-layer CREATE SURFACE APPROXIMATING A CORTICAL LAYER -surface-create-sphere GENERATE A SPHERE WITH CONSISTENT VERTEX AREAS -surface-curvature CALCULATE CURVATURE OF SURFACE -surface-cut-resample RESAMPLE A CUT SURFACE -surface-distortion MEASURE DISTORTION BETWEEN SURFACES -surface-flip-lr MIRROR A SURFACE THROUGH THE YZ PLANE -surface-flip-normals FLIP ALL TILES ON A SURFACE -surface-generate-inflated SURFACE GENERATE INFLATED -surface-geodesic-distance COMPUTE GEODESIC DISTANCE FROM ONE VERTEX TO THE ENTIRE SURFACE -surface-geodesic-distance-all-to-all COMPUTE GEODESIC DISTANCES FROM ALL VERTICES -surface-geodesic-rois DRAW GEODESIC LIMITED ROIS AT VERTICES -surface-inflation SURFACE INFLATION -surface-information DISPLAY INFORMATION ABOUT A SURFACE -surface-match SURFACE MATCH -surface-modify-sphere CHANGE RADIUS AND OPTIONALLY RECENTER A SPHERE -surface-normals OUTPUT VERTEX NORMALS AS METRIC FILE -surface-resample RESAMPLE A SURFACE TO A DIFFERENT MESH -surface-set-coordinates MODIFY COORDINATES OF A SURFACE -surface-smoothing SURFACE SMOOTHING -surface-sphere-project-unproject COPY REGISTRATION DEFORMATIONS TO DIFFERENT SPHERE -surface-sphere-triangular-patches DIVIDE STANDARD SPHERE INTO PATCHES -surface-to-surface-3d-distance COMPUTE DISTANCE BETWEEN CORRESPONDING VERTICES -surface-vertex-areas MEASURE SURFACE AREA EACH VERTEX IS RESPONSIBLE FOR -surface-wedge-volume MEASURE PER-VERTEX VOLUME BETWEEN SURFACES -unit-test UNIT TESTING -volume-all-labels-to-rois MAKE ROIS FROM ALL LABELS IN A VOLUME FRAME -volume-capture-plane INTERPOLATE IMAGE FROM PLANE THROUGH VOLUME -volume-components-to-frames CONVERT RGB/COMPLEX VOLUME TO FRAMES -volume-copy-extensions COPY EXTENDED DATA TO ANOTHER VOLUME FILE -volume-create CREATE A BLANK VOLUME FILE -volume-dilate DILATE A VOLUME FILE -volume-distortion CALCULATE VOLUME WARPFIELD DISTORTION -volume-erode ERODE A VOLUME FILE -volume-estimate-fwhm ESTIMATE FWHM SMOOTHNESS OF A VOLUME -volume-extrema FIND EXTREMA IN A VOLUME FILE -volume-fill-holes FILL HOLES IN AN ROI VOLUME -volume-find-clusters FILTER CLUSTERS BY VOLUME -volume-gradient GRADIENT OF A VOLUME FILE -volume-label-export-table EXPORT LABEL TABLE FROM VOLUME AS TEXT -volume-label-import IMPORT A LABEL VOLUME TO WORKBENCH FORMAT -volume-label-modify-keys CHANGE KEY VALUES IN A VOLUME LABEL FILE -volume-label-probability FIND FREQUENCY OF VOLUME LABELS -volume-label-to-roi MAKE A VOLUME LABEL INTO AN ROI VOLUME -volume-label-to-surface-mapping MAP A LABEL VOLUME TO A SURFACE LABEL FILE -volume-math EVALUATE EXPRESSION ON VOLUME FILES -volume-merge MERGE VOLUME FILES INTO A NEW FILE -volume-palette SET THE PALETTE OF A VOLUME FILE -volume-parcel-resampling SMOOTH AND RESAMPLE VOLUME PARCELS -volume-parcel-resampling-generic SMOOTH AND RESAMPLE VOLUME PARCELS FROM DIFFERENT VOLUME SPACE -volume-parcel-smoothing SMOOTH PARCELS IN A VOLUME SEPARATELY -volume-reduce PERFORM REDUCTION OPERATION ACROSS SUBVOLUMES -volume-remove-islands REMOVE ISLANDS FROM AN ROI VOLUME -volume-reorient CHANGE VOXEL ORDER OF A VOLUME FILE -volume-resample TRANSFORM AND RESAMPLE A VOLUME FILE -volume-rois-from-extrema CREATE VOLUME ROI MAPS FROM EXTREMA MAPS -volume-set-space CHANGE VOLUME SPACE INFORMATION -volume-smoothing SMOOTH A VOLUME FILE -volume-stats SPATIAL STATISTICS ON A VOLUME FILE -volume-tfce DO TFCE ON A VOLUME FILE -volume-to-surface-mapping MAP VOLUME TO SURFACE -volume-vector-operation DO A VECTOR OPERATION ON VOLUME FILES -volume-warpfield-affine-regression REGRESS AFFINE FROM WARPFIELD -volume-weighted-stats WEIGHTED SPATIAL STATISTICS ON A VOLUME FILE -wbsparse-merge-dense MERGE WBSPARSE FILES ALONG DENSE DIMENSION -zip-scene-file ZIP A SCENE FILE AND ITS DATA FILES -zip-spec-file ZIP A SPEC FILE AND ITS DATA FILES