Workbench:StatisticsCommands

From Van Essen Lab

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= Commands =
= Commands =
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= Statistics Commands =
= Statistics Commands =
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== caret6_stats -inferential-anova-one-way ==
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All statistics command will operate on CIFTI Scalar files containing surface-based data.  Is there ANY POSSIBILITY that these statistic command will need to operate on CIFTI Scalar files containing volume data or volume files?
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== Inferential Linear Statistics Commands ==
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=== caret6_stats -inferential-anova-one-way ===
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== caret6_stats -inferential-anova-one-way-coordinate-difference ==
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=== caret6_stats -inferential-anova-one-way-coordinate-difference ===
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== caret6_stats -inferential-interhemispheric ==
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=== caret6_stats -inferential-interhemispheric ===
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== caret6_stats -significance-cluster-threshold  MAYBE  ==
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=== caret6_stats -inferential-t-test-one-sample ===
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== caret6_stats -significance-threshold-free ==
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=== caret6_stats -inferential-t-test-paired ===
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== caret6_stats -inferential-t-test-one-sample ==
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=== caret6_stats -inferential-t-test-two-sample ===
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== caret6_stats -inferential-t-test-paired ==
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== Significance Testing Statistics Commands ==
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== caret6_stats -inferential-t-test-two-sample ==
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=== caret6_stats -significance-cluster-threshold  MAYBE  ===
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== deformation map file design ==
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=== caret6_stats -significance-threshold-free ===

Revision as of 19:37, 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 does a bunch of stuff, but primary goal is generating depth

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.


I think these have wb counterparts -- not sure:

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

All statistics command will operate on CIFTI Scalar files containing surface-based data. 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

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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