Workbench:StatisticsCommands
From Van Essen Lab
Commands
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
IMPLEMENTED: USE wb_command -file-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
METRIC FILE INFORMATION
caret_command -metric-information
<metric-file-name>
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.
DLD: Having it work on surfaces, metric, etc. would be nice. I don't think we have anything like this for borders/foci, but this also would be nice (# borders/foci; list of border/foci names). I like here how the you can extract certain info; grep; cut -f2 -d:; etc. It might be nice to more clearly delimit the columns, but I don't find myself extracting this data very often. I'm usually just i) making sure I have the right file; ii) making sure it has the right number of columns and column names; and iii) making sure the values look sane.
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
SHOW SCENE
caret_command -show-scene
<spec-file>
<scene-file>
<scene-name-or-number>
[-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
out.
% wb_command -show-scene
OFFSCREEN RENDERING OF SCENE TO AN IMAGE FILE
<scene-file>
<scene-name-or-number>
<image-file-name>
<image-width>
<image-height>
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:
bmp
ico
jpeg
jpg
png
ppm
tif
tiff
xbm
xpm
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
Note that in Workbench, there are only border projection files; there are no border files. However, each border contains two coordinates: (1) a stereotaxic coordinate which is equivalent to a unprojected border as found in a Caret5 border file and (2) a projected coordinate that may be either barycentric (projected to a relative location within a triangle) or a van essen projection (projected to an edge). The stereotaxic coordinate should always be valid while the projected coordinate may or may not be valid. A projection algorithm is in Workbench and can be used here.
% caret_command -surface-border-projection
SURFACE BORDER PROJECTION
caret_command -surface-border-projection
<coordinate-file-name>
<topology-file-name>
<input-border-file>
<output-border-projection-file>
Project the borders using the specified surface.
Run "caret_command -help-global-options"
for parameters available to all commands.
caret_command -surface-border-unprojection
An unprojection algorithm is in Workbench and can be used here.
% caret_command -surface-border-unprojection
SURFACE BORDER UNPROJECTION
caret_command -surface-border-unprojection
<coordinate-file-name>
<topology-file-name>
<input-border-projection-file>
<output-border-file>
Unproject the borders using the specified surface.
Run "caret_command -help-global-options"
for parameters available to all commands.
caret_command -surface-border-draw-around-roi
Probably can incorporate the algorithm from Caret5.
This exists as wb_command -metric-rois-to-border. Its implementation is new, and makes multipart borders for rois that have multiple pieces.
$ wb_command -metric-rois-to-border
DRAW BORDERS AROUND METRIC ROIS
wb_command -metric-rois-to-border
<surface>
<metric>
<class-name>
<border-out>
[-placement]
<fraction>
[-column]
<column>
For each ROI column, finds all edges on the mesh that cross the boundary
of the ROI, and draws borders through them. By default, this is done on
all columns in the input file, using the map name as the name for the
border.
Descriptions of parameters and options:
<surface> - the surface to use for neighbor information
<metric> - the input metric containing ROIs
<class-name> - the name to use for the class of the output borders
<border-out> - output - the output border file
[-placement] - set how far along the edge border points are drawn
<fraction> - fraction along edge from inside node (default 0.33)
[-column] - select a single column
<column> - the column number or name
% caret_command -surface-border-draw-around-roi
SURFACE BORDER DRAW AROUND ROI
caret_command -surface-border-draw-around-roi
<coordinate-file-name>
<topology-file-name>
<region-of-interest-file-name>
<input-border-projection-file-name>
<output-border-projection-file-name>
<border-name>
[-output-all-borders]
[-start-near-focus foci-projection-file-name focus-name]
Draw a border around a surface region of interest.
By default, if there is more than one disjoint region in
the ROI, only the border with the greatest number of links
is output.
If the "-output-all-borders" option is specified, the
borders for ALL disjoint regions are output.
If the "-start-near-focus" option is specified, all
borders are set up so that the first link in the border is
the link nearest the focus. This option is only applied if
"-output-all-borders" is NOT specified.
Note: The input border projection file does not need to exist.
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. See not in border projection command.
Foci projection is in Workbench.
% caret_command -surface-foci-projection
SURFACE FOCI PROJECTION
caret_command -surface-foci-projection
<coordinate-file-name>
<topology-file-name>
<input-foci-file-name>
<output-foci-projection-file-name>
[-project-onto-surface onto-surface-above-distance]
Project the foci to the surface and save into the foci
projection file.
"-project-onto-surface" is used to project the foci so that
they are a specified distance above the surface.
caret_command -surface-foci-unprojection
Foci unprojection is in Workbench.
% caret_command -surface-foci-unprojection
SURFACE FOCI UNPROJECTION
caret_command -surface-foci-unprojection
<coordinate-file-name>
<topology-file-name>
<input-foci-projection-file-name>
<output-foci-file-name>
Unproject the foci projections to the surface and save
the foci file.
caret_command -surface-folding-measures
Probably can copy from Caret5 but will need some updating.
% caret_command -surface-folding-measures
SURFACE FOLDING MEASURES
caret_command -surface-folding-measures
<coordinate-file-name>
<topology-file-name>
<output-text-report-file-name>
[-roi region-of-interest-file-name]
[-metric output-metric-measurements-file-name]
Generate a report of folding measurements on a surface.
If an ROI is provided, the folding measurements are
limited to that region of the surface.
If a metric measurements file is added, it will be output
and contain folding measurements at each node.
Node Selection: All Nodes
Surface: FIDUCIAL Human.colin.Cerebral.R.FIDUCIAL.SPM2.03-12.71723.coord
Topology: CLOSED Human.colin.Cerebral.R.CLOSED.71723.topo
71558 of 71723 nodes in region of interest
Total Surface Area: 110607.9
Region of Interest Surface Area: 110607.8
Region of Interest Center of Gravity: 32.0273 -18.2753 17.5317
Region Mean Distance Between Nodes: 1.30117
Intrinsic Curvature Index (ICI) 0.01244
Negative Intrinsic Curvature Index (NICI) -0.01081
Gaussian L2 Norm (GLN) 0.00458
Absolute Intrinsic Curvature Index (AICI) 0.02325
Mean Curvature Index (MCI) 0.07362
Negative Mean Curvature Index (NMCI) -0.06083
Mean L2 Form (MLN) 0.03025
Absolute Mean Curvature Index (AMCI) 0.13444
Folding Index (FI) 0.08535
Curvedness Index (CI) 0.20367
Shape Index (SI) 0.92224
Area Fraction of ICI (FICI) 0.46345
Area Fraction Negative ICI (FICI) 0.53655
Area Fraction of MCI (FMCI) 0.58546
Area Fraction of Neg MCI (FNMCI) 0.41454
SH2SH 0.22501
SK2SK 0.19713
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-identify-sulci SURFACE IDENTIFY SULCI
caret_command -surface-identify-sulci
<spec-file-name>
<structure>
<segmentation-volume-file-name>
<closed-topology-file-name>
<raw-coordinate-file-name>
<fiducial-coordinate-file-name>
<volume-write-type>
Identify Sulci with shape and paint.
Create a surface shape file containing depth and curvature measurements,
a paint file identifying the sulci, and an area color file. If there
is no raw coordinate file, specify fiducial coordinate file instead.
NOTE: This command MUST be run in the directory containing the files.
structure Specifies the brain structure.
Acceptable values are RIGHT or LEFT
write-volume-type Type of volume files to write.
Specifies the type of the volume files that will be written
during the segmentation process. Valid values are:
AFNI
NIFTI
NIFTI_GZIP (RECOMMENDED!!!!)
SPM
WUNIL
caret_command -surface-region-of-interest-selection
This is a big command but may be able to use "wb_command -metric-math"
TSC: Selection logic and thresholding can be done with -metric-math and related, what do people think about separate commands to put things like surface coordinates, distance from coordinate, etc into metric files, and then use -metric-math to do the combination? I'm not sure about "boundary-only", that could be another command, if it is needed...
% caret_command -surface-region-of-interest-selection
SURFACE REGION OF INTEREST SELECTION
caret_command -surface-region-of-interest-selection
<input-coord-file-name>
<input-topology-file-name>
<input-region-of-interest-file-name.roi>
<output-region-of-interest-file-name.roi>
[-all-nodes]
[-border-projection
border-projection-file-name
border-projection-name
surface-view
dimension
z-minimum
SEL-TYPE]
[-boundary-only]
[-dilate iterations]
[-dilate-paint paint-file-name column paint-name iterations]
[-edges SEL-TYPE]
[-erode iterations]
[-limit-x-lateral x-value]
[-limit-x-medial x-value]
[-limit-x-min x-value]
[-limit-x-max x-value]
[-limit-y-min y-value]
[-limit-y-max y-value]
[-limit-z-min z-value]
[-limit-z-max z-value]
[-limit-x-min-focus fociProjectionFile focusName]
[-limit-x-max-focus fociProjectionFile focusName]
[-limit-y-min-focus fociProjectionFile focusName]
[-limit-y-max-focus fociProjectionFile focusName]
[-limit-z-min-focus fociProjectionFile focusName]
[-limit-z-max-focus fociProjectionFile focusName]
[-metric metric-file-name column min max SEL-TYPE]
[-invert-selection]
[-latlon file-name column min-lat max-lat min-lon max-lon SEL_TYPE]
[-paint paint-file-name column paint-name SEL-TYPE]
[-remove-islands]
[-shape shape-file-name column min max SEL-TYPE]
The input region of interest file does not need to exist.
Perform a surface node region of interest selection
SEL-TYPE is one of
NORMAL Applies selection to all nodes.
AND And (intersection) new selection with the
existing selection.
OR Or (union) new selection with the
existing selection.
ANDNOT And the inverse of the new selection with
existing selection.
OPERATIONS
"-all-nodes" will place all connected nodes into the ROI.
"-border-projection" will place nodes that are inside of
the border into the ROI. When "dimension" is 3D, nodes
within the border and whose screen Z-coordinate is greater
than "z-minimum" are assigned to the ROI. In most cases,
a "z-minimum" of zero is sufficient. If areas within the
border are not assigned, load the surface, click the mouse
on the unassigned nodes to find the value needed for
"z-minimum" and create the ROI again.
"surface-view" is one of these single characters:
A - Anterior
D - Dorsal
L - Lateral
M - Medial
P - Posterior
R - Reset (default view)
V - Ventral
"dimension" is one of:
2D
3D
"-boundary-only" will retain only those nodes that have
at least one neighbor that is NOT in the ROI (interior
nodes are removed).
"-dilate" will dilate the ROI for the specified iterations.
"-dilate-paint" will dilate the ROI but only nodes that have
the specified paint are added to the ROI.
"-erode" will erode the ROI for the specified iterations.
"-invert-selection" will invert the node selection.
"-latlon" will add nodes to the ROI if the nodes lat/long values
are within the specified range of the column.
"-metric" will add nodes to the ROI if the nodes metric value
is within the specified range of the column.
"-paint" will add nodes to the ROI if the nodes paint name
is the specified paint name for the column.
"-remove-islands" will retain only largest set of
connected nodes in the ROI.
"-shape" will add nodes to the ROI if the nodes shape value
is within the specified range of the column.
NOTES:
The optional parameters (those enclosed in square
brackets) are performed in the order they are
listed on the command line.
"column" is either the number of the column, which
starts at one, or the name of the column. If a
a name contains spaces, it must be enclosed in double
quotes. Name has priority over number.
When finding nodes enclosed inside a border projection
use a dimension of 2D for flat surfaces. When the
dimension is 2D, the surface view is ignored.
For three dimensional surfaces (fiducial, inflated,
spherical, etc.), set the dimension to 3D. When determining
nodes within a border projection on a 3D surface, the
surface-view is applied and those nodes with a Z-coordinate
that is greater than Z-coordinate of the center of gravity
and within the border projection are added to the region
of interest.
When limits are specified with foci, the last focus
with "focus-name" found in the file is used.
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-to-segmentation-volume
SURFACE TO SEGMENTATION VOLUME
caret_command -surface-to-segmentation-volume
<input-coordinate-file-name>
<input-topology-file-name>
<output-volume-file-name>
[structure-name]
Intersect a surface with a volume and create a segmentation
volume.
The coordinate file must have its structure set to
one of "left" or "right" or else the command will
terminate with an error message. The structure may
be specified with the optional "structure-name"
parameter.
The output volume file must exist and it must be in the
same stereotaxic space as the surface. A volume file may
be created by using the "-volume-create" command.
"structure-name" is optional and must be one of
"left" or "right".
caret_command -surface-topology-disconnect-nodes
Probably can copy from Caret5 but will need some updating.
caret_command -surface-topology-disconnect-nodes
SURFACE TOPOLOGY DISCONNECT NODES
caret_command -surface-topology-disconnect-nodes
<input-topology-file-name>
<output-topology-file-name>
<region-of-interest-file-name>
Disconnect all nodes that are in the region of interest.
caret_command -volume-create
IMPLEMENTED: wb_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.
There were two volume create commands in Caret5.
% caret_command -volume-create
VOLUME CREATE
caret_command -volume-create
<x-dimension>
<y-dimension>
<z-dimension>
<output-volume-file-name-and-label>
Create a volume using the specified dimensions.
% caret_command -volume-create-in-stereotaxic-space
VOLUME CREATE IN STEREOTAXIC SPACE
caret_command -volume-create-in-stereotaxic-space
<STEREOTAXIC-SPACE>
<output-volume-file-name-and-label>
Create a volume in the specified stereotaxic space.
Valid spaces are:
AFNI
FLIRT
FLIRT-222
MACAQUE-F6
MACAQUE-F99
MRITOTAL
SPM
SPM95
SPM96
SPM99
SPM2
SPM5
T88
711-2B
711-2B-111
711-2B-222
711-2B-333
711-2C
711-2C-111
711-2C-222
711-2C-333
711-2O
711-2O-111
711-2O-222
711-2O-333
711-2Y
711-2Y-111
711-2Y-222
711-2Y-333
caret_command -volume-set-origin
IMPLEMENTED: wb_command -volume-set-space
Create a command that allows user to update a volume file's attributes (origin/spacing).
% caret_command -volume-set-origin
VOLUME SET ORIGIN
caret_command -volume-set-origin
<input-volume-file-name>
<output-volume-file-name>
<x-axis-origin-at-center-of-first-voxel>
<y-axis-origin-at-center-of-first-voxel>
<z-axis-origin-at-center-of-first-voxel>
Set the origin for the volume file.
caret_command -volume-set-spacing
IMPLEMENTED: wb_command -volume-set-space
See above.
TSC: these should be rolled into one command that just sets the entire sform
% caret_command -volume-set-spacing
VOLUME SET SPACING
caret_command -volume-set-spacing
<input-volume-file-name>
<output-volume-file-name>
<x-axis-spacing>
<y-axis-spacing>
<z-axis-spacing>
Set the spacing for the volume file.
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
--------------000000000000000000111111111111111112222222222222222
8776554432211-00122334456677899001223345566788990112234455677889
2604826048260428406273951739517395173951739517395173951738406284
Maximum Y-Value: 2067064.0
Max Y-Value Displayed: 353863.0
caret_command -volume-information
IMPLEMENTED: USE wb_command -file-information
See metric-information near top.
% caret_command -volume-information Glasser_PilotIII1.nii.gz Volume File: Glasser_PilotIII1.nii.gz dimensions: 182, 218, 182, 1 spacing: 1, 1, 1 origin (center of first voxel): -91, -126, -72 orientation: Left to Right, Posterior to Anterior, Inferior to Superior label: Glasser_PilotIII1.nii.gz voxel range: -81.9866, 300.289
caret_command -volume-information-nifti
IMPLEMENTED: USE wb_command -file-information
TSC: also of note is -nifti-information, which can print the header in a fairly raw form
See metric-information near top.
% caret_command -volume-information Glasser_PilotIII1.nii.gz
Volume File: Glasser_PilotIII1.nii.gz
dimensions: 182, 218, 182, 1
spacing: 1, 1, 1
origin (center of first voxel): -91, -126, -72
orientation: Left to Right, Posterior to Anterior, Inferior to Superior
label: Glasser_PilotIII1.nii.gz
voxel range: -81.9866, 300.289
noodle 60 % caret_command -volume-information-nifti Glasser_PilotIII1.nii.gz
sizeof_hdr: 348
data_type:
db_name:
extents: 0
session_error: 0
regular: r
dim_info: 0
dim: 3 182 218 182 1 1 1 1
intent_p1: 0.000
intent_p2: 0.000
intent_p3: 0.000
intent_code: 0
datatype: 16
bitpix: 32
slice_start: 0
pixdim: -1.000 1.000 1.000 1.000 1.000 0.000 0.000 0.000
vox_offset: 352.000
scl_slope: 1.000
scl_inter: 0.000
slice_end: 0
slice_code: 0
xyzt_units: 10
cal_max: 0.000
cal_min: 0.000
slice_duration: 0.000
toffset: 0.000
glmax: 0
glmin: 0
description: FSL4.0
aux_file:
qform_code: 4
sform_code: 4
quatern_b: 0.000
quatern_c: 1.000
quatern_d: 0.000
qoffset_x: 90.000
qoffset_y: -126.000
qoffset_z: -72.000
srow_x: -1.000 0.000 0.000 90.000
srow_y: 0.000 1.000 0.000 -126.000
srow_z: 0.000 0.000 1.000 -72.000
intent_name:
magic: n+1
Intent Name: NIFTI_INTENT_NONE
Intent Parameters:None
First Voxel XYZ (method 1): 0.000, 0.000, 0.000
Spacing: 1.000, 1.000, 1.000
QFORM: NIFTI_XFORM_MNI_152
-1.000 0.000 0.000 0.000
0.000 1.000 0.000 0.000
0.000 0.000 1.000 0.000
0.000 0.000 0.000 1.000
Orientation: Right to Left, Posterior to Anterior, Inferior to Superior
First Voxel XYZ (Method 2): 90.000, -126.000, -72.000
Spacing: -1.000, 1.000, -1.000
SFORM: NIFTI_XFORM_MNI_152
-1.000 0.000 0.000 90.000
0.000 1.000 0.000 -126.000
0.000 0.000 1.000 -72.000
0.000 0.000 0.000 1.000
Orientation: Right to Left, Posterior to Anterior, Inferior to Superior
First Voxel XYZ (Method 3): 90.000, -126.000, -72.000
Spacing: -1.000, 1.000, 1.000
Data Type: NIFTI_TYPE_FLOAT32
Space Units: NIFTI_UNITS_MM
Time Units: NIFTI_UNITS_SEC
caret_command -metric-composite
Use wb_command -metric-merge (similar exist for cifti, volume, and label).
% caret_command -metric-composite
METRIC FILE COMPOSITE ALL COLUMNS
caret_command -metric-composite
<output-metric-file>
<input-metric-files...>
Concatenate all columns from the input metric files and place
them into the output metric file
caret_command -metric-composite-identified-columns
Use wb_command -metric-merge (similar exist for cifti, volume, and label).
% caret_command -metric-composite-identified-columns
METRIC COMPOSITE IDENTIFIED COLUMNS
caret_command -metric-composite-identified-columns
<output-metric-file-name>
[input-metric-file-1 file-1-column]
...
[input-metric-file-N file-2-column]
Composite the selected columns from the input metric
files and place them into the output metric file.
"column" is either the number of the column, which
starts at one, or the name of the column. If a
a name contains spaces, it must be enclosed in double
quotes. Name has priority over number.
caret_command -metric-math-postfix
Use wb_command -metric-math (similar exist for cifti and volume).
% caret_command -metric-math-postfix
METRIC MATH POSTFIX
caret_command -metric-math-postfix
<input-metric-file-name>
<output-metric-file-name>
<output-column-name-number>
<postfix-expression-within-double-quotes>
Perform mathematical operations on a metric file. The
mathematical expression must be in post-fix (reverse
polish notation). See
http://en.wikipedia.org/wiki/Reverse_Polish_notation
The postfix expression must be in double quotes. Otherwise,
operators, such as "*" will match all files in the
current directory.
A metric column is identified by a sequence of characters
the are immediately proceeded and immediately followed by
an at-sign (@).
These characters are either the name of the metric column or
the number of the metric column which starts at one. To use
a metric column that is in a metric file other than the input
metric file, start with an at-sign, followed by the name of
the metric file, followed by a colon (:),
followed by the identifier of the metric column, and lastly,
an at-sign.
Spaces are allowed in file names or column identifiers:
Example "@test file::subject 2@"
Examples (for the column named "activation" located in:
the file named "experiment.metric"
@activation@
@experiment.metric::activation@
If the output metric column is a name and it does not exist
it will be created.
Binary operators supported are:
+ addition
- subtraction
* multiplication
/ division
^ exponention
max2 maximum-value
min2 minimum-value
Unary operations supported are:
abs absolute-value
exp exponential function
flipsign flip the sign
log natural log
log2 base 2 logarithm
log10 base 10 logarithm
sqrt square root
Predefined values from each nodes metric values
nodeavg Average value at each node
nodemax Maximum value at each node
nodemin Minimum value at each node
nodesum Sum of values at each node
Example: "5 1 2 + 4 * + 3 -"
Infix => ((1 + 2) * 4 + 5 - 3)
evaluates to 14.
Example: "2 3 * 2 3 + min2"
Infix => min2(2 * 3, 2 + 3)
evaluates to 5.
Example: "@one@ @two@ add"
adds the columns named "one" and "two".
caret_command -metric-set-column-name
Use wb_command -set-map-names.
% caret_command -metric-set-column-name
METRIC SET COLUMN NAME
caret_command -metric-set-column-name
<metric-file-name>
[column new-name]
Rename columns in a metric file.
"column" is either the number of the column, which
starts at one, or the name of the column. If a
a name contains spaces, it must be enclosed in double
quotes. Name has priority over number.
caret_command -metric-set-column-to-scalar
Use wb_command -metric-math (similar exist for cifti and volume).
% caret_command -metric-set-column-to-scalar
METRIC SET COLUMN TO SCALAR
caret_command -metric-set-column-to-scalar
<metric-file-name>
[column scalar-value]
Set columns to a scalar value in a metric file.
"column" is either the number of the column, which
starts at one, or the name of the column. If a
a name contains spaces, it must be enclosed in double
quotes. Name has priority over number. If a name is
used for a column and the column does not exist it will
be created.
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
ANOVA One-Way
-inferential-anova-one-way
<-data-file group-name input-file-name>
<-output-statistic-file output-statistic-file-name>
[-add-f-statistic-p-value]
[-add-f-statistic-q-value]
[-add-f-statistic-numerator-degrees-of-freedom]
[-add-f-statistic-denominator-degrees-of-freedom]
[-output-randomized-file output-randomized-file-name]
[-randomized-iterations number-of-iterations]
[-output-file-encoding encoding-type]
[-randomized-output-file-encoding encoding-type]
[-random-seed random-seed-value]
Perform a One-Way Analysis of Variance on the means of
data groups.
There must be at least two groups of data. The data for
a group may be in more than one file. The "group-name"
associates a data file with a group.
The default name for the column in the output file
containing the F-Statistic is F-Statistic
If the "-output-randomized-file" option is specified, a
file is written that includes "number-of-iterations"
data columns containing F-Statistics for shuffled input
data columns. This file is intended for use with the
significance determination algorithm.
P-Value is the significance computed from the F-Statistic
and the degrees of freedom.
Q-Value is (1.0 - P) and may be useful for thresholding
in Caret.
The available output file encodings are:
GIFTI
GIFTI-BASE64
GIFTI-GZIP
GIFTI-EXTERNAL
"GIFTI" is a XML file with all data in text format.
Files in this format are the largest and take the
longest time to read of the GIFTI formats.
"GIFTI-BASE64" is an XML file with the binary data
encoded as Base64 text.
"GIFTI-GZIP" is an XML file with the binary data
compressed using the the GZIP algorithm with the
binary data encoded using Base64 text. Files in this
format are smaller than the other GIFTI formats and
usually take the least time to read.
"GIFTI-EXTERNAL" is an XML file with the data stored
in an separate, external, uncompressed file.
The default output file encoding is GIFTI-GZIP
The default output randomized file encoding is GIFTI-GZIP
The random seed sets the seed of the random number
generator which affects the sequence of numbers that
are generated. If a command is run with with
identical inputs and the command uses the random number
generator, the results will be identical only if the
random-seed-value is set using the same value. The seed
used should be a large integer value.
caret6_stats -inferential-anova-one-way-coordinate-difference
$ caret6_stats -inferential-anova-one-way-coordinate-difference
ANOVA One-Way Coordinate Difference
-inferential-anova-one-way-coordinate-difference
<-data-file group-name input-coordinate-file-name>
<-output-statistic-file output-statistic-file-name>
[-add-f-statistic-p-value]
[-add-f-statistic-q-value]
[-add-f-statistic-numerator-degrees-of-freedom]
[-add-f-statistic-denominator-degrees-of-freedom]
[-output-randomized-file output-randomized-file-name]
[-randomized-iterations number-of-iterations]
[-output-file-encoding encoding-type]
[-randomized-output-file-encoding encoding-type]
[-random-seed random-seed-value]
Perform a One-Way Analysis of Variance on the Coordinate
Differences.
There must be at least two groups of data.
The default name for the column in the output file
containing the F-Statistic is F-Statistic
If the "-output-randomized-file" option is specified, a
file is written that includes "number-of-iterations"
data columns containing F-Statistics for shuffled input
coordinate differences. This file is intended for use
with a significance determination algorithm.
P-Value is the significance computed from the F-Statistic
and the degrees of freedom.
Q-Value is (1.0 - P) and may be useful for thresholding
in Caret.
The available output file encodings are:
GIFTI
GIFTI-BASE64
GIFTI-GZIP
GIFTI-EXTERNAL
"GIFTI" is a XML file with all data in text format.
Files in this format are the largest and take the
longest time to read of the GIFTI formats.
"GIFTI-BASE64" is an XML file with the binary data
encoded as Base64 text.
"GIFTI-GZIP" is an XML file with the binary data
compressed using the the GZIP algorithm with the
binary data encoded using Base64 text. Files in this
format are smaller than the other GIFTI formats and
usually take the least time to read.
"GIFTI-EXTERNAL" is an XML file with the data stored
in an separate, external, uncompressed file.
The default output file encoding is GIFTI-GZIP
The default output randomized file encoding is GIFTI-GZIP
The random seed sets the seed of the random number
generator which affects the sequence of numbers that
are generated. If a command is run with with
identical inputs and the command uses the random number
generator, the results will be identical only if the
random-seed-value is set using the same value. The seed
used should be a large integer value.
caret6_stats -inferential-interhemispheric
$ caret6_stats -inferential-interhemispheric
Interhemispheric
-inferential-interhemispheric
<-data-file-left-A left-group-A-input-file-name>
<-data-file-left-B left-group-B-input-file-name>
<-data-file-right-A right-group-A-input-file-name>
<-data-file-right-B right-group-B-input-file-name>
<-output-statistic-file output-statistic-file-name>
<-pooled | -unpooled>
[-add-t-statistic-p-value]
[-add-t-statistic-q-value]
[-add-t-statistic-degrees-of-freedom]
[-output-randomized-file output-randomized-file-name]
[-randomized-iterations-within number-of-iterations]
[-randomized-iterations-between number-of-iterations]
[-variance-smoothing-coordinate-file coord-file-name]
[-variance-smoothing-topology-file topo-file-name]
[-variance-smoothing-strength strength]
[-variance-smoothing-iterations iterations]
[-output-file-encoding encoding-type]
[-randomized-output-file-encoding encoding-type]
[-random-seed random-seed-value]
Perform a test to identify asymmetry between the left
and right hemispheres. A T-Test is performed between
the left hemisphere files and another T-Test is performed
between the right hemisphere files. The output file
contains the product of these two T-Test files.
The default name for the column in the output file
containing the product of the T-Statistics is "T-Statistic-Product".
If the variances of the data in the two groups are the
same use "-pooled". If the variances of the data in
the two groups are different, use "-unpooled".
If the "-output-randomized-file" option is specified, a
randomized file for significance testing is created.
First, a file is created containing columns that are
T-Statistics for randomized combinations of columns from
the left hemisphere files. The number of columns is
specified by the "-randomized-iterations-within" option.
Second, a file is created containing columns that are
T-statistics for randomized combinations of columns from
the right hemisphere files. The number of columns is
specified by the "-randomized-iterations-within" option.
Third, a file is created that contains the product of
a random selection from the left hemisphere file multiplied
by a random selection from the right hemisphere file. The
number of columns is specified by using the
"-randomized-iterations-between" option.
P-Value is the significance computed from the T-Statistic
and the degrees of freedom.
Q-Value is (1.0 - P) and may be useful for thresholding
in Caret.
DOF is the degrees of freedom.
The available output file encodings are:
GIFTI
GIFTI-BASE64
GIFTI-GZIP
GIFTI-EXTERNAL
"GIFTI" is a XML file with all data in text format.
Files in this format are the largest and take the
longest time to read of the GIFTI formats.
"GIFTI-BASE64" is an XML file with the binary data
encoded as Base64 text.
"GIFTI-GZIP" is an XML file with the binary data
compressed using the the GZIP algorithm with the
binary data encoded using Base64 text. Files in this
format are smaller than the other GIFTI formats and
usually take the least time to read.
"GIFTI-EXTERNAL" is an XML file with the data stored
in an separate, external, uncompressed file.
The default output file encoding is GIFTI-GZIP
The default output randomized file encoding is GIFTI-GZIP
The random seed sets the seed of the random number
generator which affects the sequence of numbers that
are generated. If a command is run with with
identical inputs and the command uses the random number
generator, the results will be identical only if the
random-seed-value is set using the same value. The seed
used should be a large integer value.
caret6_stats -inferential-t-test-one-sample
$ caret6_stats -inferential-t-test-one-sample
T-Test One-Sample
-inferential-t-test-one-sample
<-data-file input-file-name>
<-output-statistic-file output-statistic-file-name>
<-hypothesis-mean value>
[-add-t-statistic-p-value]
[-add-t-statistic-q-value]
[-add-t-statistic-degrees-of-freedom]
[-output-randomized-file output-randomized-file-name]
[-randomized-iterations number-of-iterations]
[-variance-smoothing-surface-file surface-file-name]
[-variance-smoothing-coordinate-file coord-file-name]
[-variance-smoothing-topology-file topo-file-name]
[-variance-smoothing-strength strength]
[-variance-smoothing-iterations iterations]
[-output-file-encoding encoding-type]
[-randomized-output-file-encoding encoding-type]
[-random-seed random-seed-value]
Perform a One-Sample T-Test testing the means against
the hypothesis mean.
The input data may be in more than one file. Just use
multiple instances of "-data-file" for each file.
The default name for the column in the output file
containing the T-Values is T-Statistic
If the "-output-randomized-file" option is specified, a
file is written that includes "number-of-iterations"
data columns containing T-Statistics for shuffled input
data columns (random columns have sign flipped. This
file is intended for use with the significance
determination algorithm.
P-Value is the significance computed from the T-Statistic
and the degrees of freedom.
Q-Value is (1.0 - P) and may be useful for thresholding
in Caret.
DOF is the degrees of freedom.
The available output file encodings are:
GIFTI
GIFTI-BASE64
GIFTI-GZIP
GIFTI-EXTERNAL
"GIFTI" is a XML file with all data in text format.
Files in this format are the largest and take the
longest time to read of the GIFTI formats.
"GIFTI-BASE64" is an XML file with the binary data
encoded as Base64 text.
"GIFTI-GZIP" is an XML file with the binary data
compressed using the the GZIP algorithm with the
binary data encoded using Base64 text. Files in this
format are smaller than the other GIFTI formats and
usually take the least time to read.
"GIFTI-EXTERNAL" is an XML file with the data stored
in an separate, external, uncompressed file.
The default output file encoding is GIFTI-GZIP
The default output randomized file encoding is GIFTI-GZIP
The random seed sets the seed of the random number
generator which affects the sequence of numbers that
are generated. If a command is run with with
identical inputs and the command uses the random number
generator, the results will be identical only if the
random-seed-value is set using the same value. The seed
used should be a large integer value.
caret6_stats -inferential-t-test-paired
$ caret6_stats -inferential-t-test-paired
T-Test Paired
-inferential-t-test-paired
<-data-file group-name input-file-name>
<-output-statistic-file output-statistic-file-name>
[-add-t-statistic-p-value]
[-add-t-statistic-q-value]
[-add-t-statistic-degrees-of-freedom]
[-output-randomized-file output-randomized-file-name]
[-randomized-iterations number-of-iterations]
[-variance-smoothing-surface-file surface-file-name]
[-variance-smoothing-coordinate-file coord-file-name]
[-variance-smoothing-topology-file topo-file-name]
[-variance-smoothing-strength strength]
[-variance-smoothing-iterations iterations]
[-output-file-encoding encoding-type]
[-randomized-output-file-encoding encoding-type]
[-random-seed random-seed-value]
Perform a Paired T-Test.
A paired T-Test determines if measurements on participants
have changed after some event. Essentially, the second
data group's scores are subtracted from the first data
group's scores and a one-sample T-Test is performed with
an hypothesis mean of zero.
There must be exactly two data groups. Each participant
must be in both data groups and in the same position in
the two data groups (subject X must be the i'th metric
column in both of the data groups).
The input data may be in more than one file. Just use
multiple instances of "-data-file" for each file.
The default name for the column in the output file
containing the T-Values is T-Statistic
If the "-output-randomized-file" option is specified, a
file is written that includes "number-of-iterations"
data columns containing T-Statistics for shuffled input
data columns (random columns have sign flipped. This
file is intended for use with the significance
determination algorithm.
P-Value is the significance computed from the T-Statistic
and the degrees of freedom.
Q-Value is (1.0 - P) and may be useful for thresholding
in Caret.
DOF is the degrees of freedom.
The available output file encodings are:
GIFTI
GIFTI-BASE64
GIFTI-GZIP
GIFTI-EXTERNAL
"GIFTI" is a XML file with all data in text format.
Files in this format are the largest and take the
longest time to read of the GIFTI formats.
"GIFTI-BASE64" is an XML file with the binary data
encoded as Base64 text.
"GIFTI-GZIP" is an XML file with the binary data
compressed using the the GZIP algorithm with the
binary data encoded using Base64 text. Files in this
format are smaller than the other GIFTI formats and
usually take the least time to read.
"GIFTI-EXTERNAL" is an XML file with the data stored
in an separate, external, uncompressed file.
The default output file encoding is GIFTI-GZIP
The default output randomized file encoding is GIFTI-GZIP
The random seed sets the seed of the random number
generator which affects the sequence of numbers that
are generated. If a command is run with with
identical inputs and the command uses the random number
generator, the results will be identical only if the
random-seed-value is set using the same value. The seed
used should be a large integer value.
caret6_stats -inferential-t-test-two-sample
$ caret6_stats -inferential-t-test-two-sample
T-Test Two-Sample
-inferential-t-test-two-sample
<-data-file group-name input-file-name>
<-output-statistic-file output-statistic-file-name>
<-pooled | -unpooled>
[-add-t-statistic-p-value]
[-add-t-statistic-q-value]
[-add-t-statistic-degrees-of-freedom]
[-output-randomized-file output-randomized-file-name]
[-randomized-iterations number-of-iterations]
[-variance-smoothing-surface-file surface-file-name]
[-variance-smoothing-coordinate-file coord-file-name]
[-variance-smoothing-topology-file topo-file-name]
[-variance-smoothing-strength strength]
[-variance-smoothing-iterations iterations]
[-output-file-encoding encoding-type]
[-randomized-output-file-encoding encoding-type]
[-random-seed random-seed-value]
Perform a Two-Sample T-Test on the means of the two
data groups.
If the variances of the data in the two groups are the
same use "-pooled". If the variances of the data in
the two groups are different, use "-unpooled".
There must be exactly two groups of data. The data for
a group may be in more than one file. The "group-name"
associates a data file with a group.
The default name for the column in the output file
containing the T-Values is T-Statistic
If the "-output-randomized-file" option is specified, a
file is written that includes "number-of-iterations"
data columns containing T-Statistics for shuffled input
data columns. This file is intended for use with the
significance determination algorithm.
P-Value is the significance computed from the T-Statistic
and the degrees of freedom.
Q-Value is (1.0 - P) and may be useful for thresholding
in Caret.
DOF is the degrees of freedom.
The available output file encodings are:
GIFTI
GIFTI-BASE64
GIFTI-GZIP
GIFTI-EXTERNAL
"GIFTI" is a XML file with all data in text format.
Files in this format are the largest and take the
longest time to read of the GIFTI formats.
"GIFTI-BASE64" is an XML file with the binary data
encoded as Base64 text.
"GIFTI-GZIP" is an XML file with the binary data
compressed using the the GZIP algorithm with the
binary data encoded using Base64 text. Files in this
format are smaller than the other GIFTI formats and
usually take the least time to read.
"GIFTI-EXTERNAL" is an XML file with the data stored
in an separate, external, uncompressed file.
The default output file encoding is GIFTI-GZIP
The default output randomized file encoding is GIFTI-GZIP
The random seed sets the seed of the random number
generator which affects the sequence of numbers that
are generated. If a command is run with with
identical inputs and the command uses the random number
generator, the results will be identical only if the
random-seed-value is set using the same value. The seed
used should be a large integer value.
Significance Testing Statistics Commands
caret6_stats -significance-cluster-threshold MAYBE
$ caret6_stats -significance-cluster-threshold
Signficance - Cluster-based Thresholding
-significance-cluster-threshold
<-statistic-file statistic-file-name>
<-statistic-file-column column-name-or-index>
<-output-statistic-file output-file-name>
<-random-file randomized-file-name>
<-coordinate-file coordinate-file-name>
<-topology-file topology-file-name>
<-significance-level value>
<-threshold-negative value>
<-threshold-positive value>
<-output-label-file label-file-name>
<-output-report-file report-file-name>
[-distortion-file distortion-metric-shape-file-name]
[-distortion-file-column column-name-or-index]
[-number-of-threads number-of-threads-to-run
[-print-progress-message]
[-output-file-encoding encoding-type]
[-randomized-output-file-encoding encoding-type]
Perform cluster-based thresholding.
* Using the thresholds, find clusters in the specified
column of the input data file.
* Using the thresholds, find the largest cluster in
each column of the randomized file. Sort these
clusters using their surface area from largest to
smallest.
* For each cluster in the input data file, use its
surface area to find its ranking in the sorted
clusters from the randomized file to determine the
input data file's cluster's P-Value. For example,
if it falls at the 8th percentile, it receives a
P-Value of 0.08.
* The output file will contain the data column from
the input file and one or both of the P-Value and
One-Minus-P-Value.
The data file column may be specified by either its name
or by its column index with the first column at index 1.
The surface used during this process is either a surface
file specified with the "-surface-file" option or
coordinate and topology files specified with the
"-coordinate-file" and "-topology-file" options.
One or both of the "add-p-value" and
"-add-one-minus-p-value" options must be specified.
The "-add-one-minus-p-value" option works best for
thresholding in Caret. The column names may be empty
(two consecutive double quotes) in which case the default
names are used.
If the number-of-threads-to-run is greater than one,
the cluster search of the randomized file is run in
parallel using the specified number of threads.
The distortion file is used to correct for surface
distortion that may occur in the case of surface
averaging. The distortion file column may be specified
with either its name or by its column index with the first
column at index 1.
If the report file name is not specified the report is
printed to the terminal.
If "-print-progress-message" is specified, a message
is printed as each randomized file column is searched
.
The available output file encodings are:
GIFTI
GIFTI-BASE64
GIFTI-GZIP
GIFTI-EXTERNAL
"GIFTI" is a XML file with all data in text format.
Files in this format are the largest and take the
longest time to read of the GIFTI formats.
"GIFTI-BASE64" is an XML file with the binary data
encoded as Base64 text.
"GIFTI-GZIP" is an XML file with the binary data
compressed using the the GZIP algorithm with the
binary data encoded using Base64 text. Files in this
format are smaller than the other GIFTI formats and
usually take the least time to read.
"GIFTI-EXTERNAL" is an XML file with the data stored
in an separate, external, uncompressed file.
The default output file encoding is GIFTI-GZIP
The default output randomized file encoding is GIFTI-GZIP
caret6_stats -significance-threshold-free
$ caret6_stats -significance-threshold-free
Signficance - Threshold Free
-significance-threshold-free
<-statistic-file statistic-file-name>
<-statistic-file-column column-name-or-index>
<-output-statistic-file output-statistic-file-name>
<-random-file randomized-file-name>
[-output-randomized-file output-random-file-name]
<-coordinate-file coordinate-file-name>
<-topology-file topology-file-name>
<-significance-level value>
<-output-label-file label-file-name>
<-output-report-file report-file-name>
[-distortion-file distortion-metric-shape-file-name]
[-distortion-file-column column-name-or-index]
[-E extent]
[-H height]
[-monotonic]
[-threshold-positive value]
[-threshold-negative value]
[-output-file-encoding encoding-type]
[-randomized-output-file-encoding encoding-type]
Set the significance levels for nodes using the threshold-
free cluster enhancement algorithm adapted for surface-
based data.
* Transform the specified column in the statistic
file using the TFCE enhancement function.
* Transform all columns in the randomized file using
the TFCE enhancement function.
* Find the greatest TFCE-enhanced value in each of the
randomized files columns. Rank these values from
largest to smallest, assigning P-Values based upon
their ranks so that the largest value has a P-Value
of 0.0 and the smallest values a P-Value of 1.0
* For each node in the specified column of the
statistic file, compare its value to the ranked
values and assign the node its P-Value.
Set threshold free significance levels.
* Find and rank the largest absolute value in each
column of the randomized file where each column is
a TFCE transformed statistic generated from.
permuted data.
* For each value in the input files TFCE column, find
its ranking in the ranked, random TFCE data and
generate the significance level (p-value).
* Add the P and/or Q values to the output file.
The statistic file column may be specified by either its
name or by its column index with the first column at
index 1.
The output randomized file is optional. Creating the
output randomized file may use so much memory that the
program will fail with an out of memory error.
The thresholds should only be used if "-monotonic"
(the slot monotonic algorithm) is being used.
The distortion file is used to correct for surface
distortion that may occur in the case of surface
averaging. The distortion file column may be specified
with either its name or by its column index with the first
column at index 1.
If "-print-progress-message" is specified, a message
is printed as each randomized file column is searched.
Add the "-monotonic" option to run the old TFCE algorithm which is very slow
The default value for "-E" (extent) is 1.0
The default value for "-H" (height) is 2.0
The available output file encodings are:
GIFTI
GIFTI-BASE64
GIFTI-GZIP
GIFTI-EXTERNAL
"GIFTI" is a XML file with all data in text format.
Files in this format are the largest and take the
longest time to read of the GIFTI formats.
"GIFTI-BASE64" is an XML file with the binary data
encoded as Base64 text.
"GIFTI-GZIP" is an XML file with the binary data
compressed using the the GZIP algorithm with the
binary data encoded using Base64 text. Files in this
format are smaller than the other GIFTI formats and
usually take the least time to read.
"GIFTI-EXTERNAL" is an XML file with the data stored
in an separate, external, uncompressed file.
The default output file encoding is GIFTI-GZIP
The default output randomized file encoding is GIFTI-GZIP
