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Are we replacing metric with Cifti Scalar?

TSC: no, processing cifti in nontrivial ways generally has to operate on each structure independently, which is far more convenient as metric files than trying to deal directly with the mappings.

NOTE: -cifti-convert is a HACK to get cifti data into cifti-unaware applications, like matlab. -cifti-create-dense-timeseries is currently the main way to create cifti from non-cifti standard data files.

JWH: I thought our plan was to use CIFTI Scalar files but restricted to those containing a single surface structure.

TSC: no, all code that deals with dense cifti mappings must have the ability to deal with multi-structure cifti, so nothing can be simpler in code when using single structure cifti. Dealing with cifti mappings is not something most algorithms should have to do, because it is generally the same each time. Thus, the code to separate dense mappings into single-structure dedicated file types (metric, label, volume) is in one place, and calculation code uses the considerably simpler dedicated file types.

caret_command -file-convert

e.g., if you want to convert to/from VTK; wb_import doesn't like some gii, and I haven't decoded why

If there is a file that is failing to convert, let us know.

wb_import is part of the Caret5 source. It may be possible to move it to the workbench source but may be a lot of work.

caret_command -metric-information

We should probably have either a "file information" command that works for any file and whose output is file dependent. An alternative is a "map information" command that works for any map file (is selectable as an overlay). For files that are mapped with a palette, the output should be very similar to the existing command since all of these files make descriptive statistics available. For files mapped with a label table, we may want to output the map indices and names and optionally the contents of the label table (keys/names).

 % caret_command -metric-information
      caret_command -metric-information  
         Display Information about a metric file's contents.

 % caret_command -metric-information composite.func.gii 
 Filename: composite.func.gii 
 Number of Nodes: 71723 
 Number of Columns: 3
 Column      Minimum      Maximum           Mean     Sample Dev     % Positive     % Negative   Column Name
      1     -685.000      873.000         29.632        154.699         15.189          7.355   Attn shifts, case 1582.R, (Corbetta et al., 1998)
      2       -6.548       10.717          0.241          1.568         13.489          7.942   Attention shifts, pop avg (Corbetta et al., 1998)
      3      -13.215        4.059         -1.511          2.039         20.430         79.570   letter decision task - Gold & Buckner 2002

TSC: I think having one command work on all file types could be fine, since it doesn't output a file.

caret_command -show-scene

There is a show scene in wb_command. We should compare output to see if any needed functionality is missing.

 % caret_command -show-scene
      caret_command -show-scene  
         [-image-file  image-file-name  images-per-row] 
         Render an image of a scene into an image file.
         Note: the scene numbers start at one.
         If the "scene-name-or-number" is numeric it is interpreted
         to be the index of the scene (1..N) in the scene file.  
         Otherwise, it is interpreted to be the name of the scene.
         If the "-image-file" option is specified, the images of
         the main and viewing windows will be placed into an image
         file.  "images-per-row" specifies how the images (if there
         are viewing windows displayed in the scene) will be layed

 % wb_command -show-scene


      Render content of browser windows displayed in a scene into image
      file(s).  The image file name should be similar to "capture.png".  If
      there is only one image to render, the image name will not change.  If
      there is more than one image to render, an index will be inserted into
      the image name: "capture_01.png", "capture_02.png" etc.

      The image format is determined by the image file extension.
      Image formats available on this sytem are:
      Note: Available image formats may vary by operating system.

      Descriptions of parameters and options:

      <scene-file> - scene file
      <scene-name-or-number> - name or number (starting at one) of the scene in
         the scene file
      <image-file-name> - output image file name
      <image-width> - width of output image(s)
      <image-height> - height of output image(s)

caret_command -surface-border-projection

A projection algorithm is in Workbench and can be used here.

caret_command -surface-border-unprojection

An unprojection algorithm is in Workbench and can be used here.

caret_command -surface-border-draw-around-roi

Probably can incorporate the algorithm from Caret5.

caret_command -surface-cell-projection

Cells are not in Workbench but are the same as foci.

caret_command -surface-cell-unprojection

Cells are not in Workbench but are the same as foci.

caret_command -surface-foci-projection

We do not have foci files in Workbench, just foci projection. wb_command only imports foci projection but could be updated for foci. Alternative is to convert foci to foci projection in Caret5.

Foci projection is in Workbench.

caret_command -surface-foci-unprojection

Foci unprojection is in Workbench.

caret_command -surface-folding-measures

Probably can copy from Caret5 but will need some updating.

caret_command -surface-identify-sulci

This is a very large, complex operation.

TSC: this is mainly needed for depth, which we are going to reengineer anyway

caret_command -surface-region-of-interest-selection

This is a big command but may be able to use "wb_command -cifti-math"

caret_command -surface-to-segmentation-volume

This is possible with wb_command -create-signed-distance-volume, followed by -volume-math 'x<0', could be provided as a separate command

caret_command -surface-topology-disconnect-nodes

Probably can copy from Caret5 but will need some updating.

caret_command -volume-create

Is there a desire to create with dimensions, spacing, origin? Name of stereotaxic space? Or both?

TSC: it should be quite easy - I would opt not to provide any standard spaces, since it is much more likely you will already have a reference volume for those.

caret_command -volume-set-origin

Create a command that allows user to update a volume file's attributes (origin/spacing).

caret_command -volume-set-spacing

See above.

TSC: these should be rolled into one command that just sets the entire sform

caret_command -volume-histogram

This should probably be generalized to work with any mappable data file (displayed as overlay) that maps with a palette.

TSC: what would the output be?

JWH: It outputs a histogram as a "text image" as shown below. The asterisks represent the distribution of the data. The numbers in the right column are the quantity. Numbers along the bottom are the voxel data values (the data ranges -81.9866 to 300.289).

TSC: do we really need this? The histogram in the gui seems better to me (granted, it is a few more clicks to get there, but when do you want a text histogram while not visualizing the file?).

% caret_command -volume-histogram Glasser_PilotIII1.nii.gz

             ***                                                 353863.0
             ***                                                 345016.4
             ***                                                 336169.8
             ***                                                 327323.3
             ***                                                 318476.7
             ***                                                 309630.1
             ***                                                 300783.6
             ***                                                 291937.0
             ***                                                 283090.4
             ***                                                 274243.8
             ***                                                 265397.2
             ***                                                 256550.7
             ***                                                 247704.1
             ***                                                 238857.5
             ***                                                 230011.0
             ***                                                 221164.4
             ***             *                                   212317.8
             ***             **                                  203471.2
             ***            ***                                  194624.7
             ***            ***                                  185778.1
             ***            ****                                 176931.5
             ***            ****                                 168084.9
             ***           *****                                 159238.4
             ***           ******                                150391.8
             ***           ******      *                         141545.2
             ****         *******      *                         132698.6
             ****         ********    ***                        123852.1
             ****        *********    ***                        115005.5
             *****      **********   ****                        106158.9
             **********************  ****                         97312.3
             *****************************                        88465.8
             *****************************                        79619.2
             *****************************                        70772.6
             *****************************                        61926.0
             ******************************                       53079.5
             ******************************                       44232.9
             *******************************                      35386.3
             ********************************                     26539.7
             *************************************                17693.2
             ****************************************              8846.6
Maximum Y-Value: 2067064.0
Max Y-Value Displayed: 353863.0

caret_command -volume-information

See metric-information near top.

caret_command -volume-information-nifti

See metric-information near top.

TSC: redundant, all volumes are nifti.

caret_command -metric-composite

Use wb_command -metric-merge (similar exist for cifti and volume, and soon for label).

caret_command -metric-composite-identified-columns

Use wb_command -metric-merge (similar exist for cifti and volume, and soon for label).

caret_command -metric-math-postfix

Use wb_command -metric-math (similar exist for cifti and volume).

caret_command -metric-set-column-name

Use wb_command -set-map-names.

caret_command -metric-set-column-to-scalar

Use wb_command -metric-math (similar exist for cifti and volume).

Statistics Commands

Will this be a new command line program "wb_stats" or will the commands be added to "wb_command"?

All statistics command will operate on CIFTI Scalar files containing surface-based data. Will there be one structure per file or multiple structures (left/right)? Is there ANY POSSIBILITY that these statistic command will need to operate on CIFTI Scalar files containing volume data or volume files?

Inferential Linear Statistics Commands

For the linear statistics commands we could reformat and solve using a General Linear Model Caret:Documentation:StatisticsGLM . However, it will be simpler just to use the standard algorithm for each statistical test (and probably best if reviewers of papers ask). Caret:Documentation:Statistics

If possible, parallel processing with OpenMP should be used. Since these commands often operate on 'vectors' of data, GPU processing (OpenCL) may be possible but this decision should be deferred.

All of these commands are in either Caret5 or Caret6 so implementation should be fairly straightforward and the previous implementations can be used to validate operation of the new commands.

caret6_stats -inferential-anova-one-way

caret6_stats -inferential-anova-one-way-coordinate-difference

caret6_stats -inferential-interhemispheric

caret6_stats -inferential-t-test-one-sample

caret6_stats -inferential-t-test-paired

caret6_stats -inferential-t-test-two-sample

Significance Testing Statistics Commands

caret6_stats -significance-cluster-threshold MAYBE

caret6_stats -significance-threshold-free

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