Workbench:StatisticsCommands

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(Statistics Commands)
(caret_command -surface-identify-sulci)
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== caret_command -surface-identify-sulci ==
== caret_command -surface-identify-sulci ==
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This does a bunch of stuff, but primary goal is generating depth
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This is a very large, complex operation.
== caret_command -surface-region-of-interest-selection ==
== caret_command -surface-region-of-interest-selection ==

Revision as of 19:51, 30 August 2013

Contents

Commands

Are we replacing metric with Cifti Scalar? Can convert metric (func) with "wb_command -cifti-convert"


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).


Filename: Glasser_PilotIII.L.T1DividedByT2_RemovedOutliers_s5.20k_fs_LR.func.gii
Number of Nodes: 20252
Number of Columns: 1
Column      Minimum      Maximum           Mean     Sample Dev     % Positive     % Negative   Column Name
    1            0.000           1.842                 1.225          0.401         91.472          0.000         Masked Myelin Map

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 -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.

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

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?

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.

caret_command -volume-histogram

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

caret_command -volume-information

See metric-information near top.

caret_command -volume-information-nifti

See metric-information near top.

caret_command -metric-composite

Use wb_command -cifti-merge.

caret_command -metric-composite-identified-columns

Use wb_command -cifti-merge.

caret_command -metric-math-postfix

Use wb_command -cifti-math.

caret_command -metric-set-column-name

Generalize to work on any mappable data file (displayed as an overlay).

caret_command -metric-set-column-to-scalar

Use wb_command -cifti-math.

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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