Differences between revisions 4 and 5
Deletions are marked like this. Additions are marked like this.
Line 44: Line 44:
||Category||Flag||Argument||Description||
||Basic options||-a|| <numberOfAverages>||Average the curvature <numberOfAverages> times.||
||Basic options||-f|| <surf_name>||Set surface (used to calculate curvature) to <surf_name>. Eg: wm, pial etc.||
||Basic options||-g||||Calculate Gaussian and Mean||
||Basic options||-l||<labelFileName>||(-L) Constrain statistics to the region defined in <labelFileName>.||
||Basic options||-n||||Normalise the curvature before computation. Normalisation takes precedence over scaling, so if '-n' is specified in conjunction with '-c' or '-smin'/'-smax' it will override the effects of the scaling.[[BR]]If specified in conjunction with '-o outputFileStem>' will also create a curvature file with these values.||
||Output||-m||||Output min / max information for the processed curvature.||
||Output||-o||<outputFileStem>||Specifies what files to output and how to name them. This includes condensed text output, histogram files (MatLAB friendly) and curvature files. See details below under ''Output Files'' heading.||
||Output||-s||<summaryCondition>||Write out stats as <summaryCondition>. (Not sure what this does -- GW)||
||Output||--writeCurvatureFiles||||Toggle (set? --GW) save flag on curvature files||
||Scaling||-c||<scaleFactor>||Scale curvature values with <factor>. The mean of the original curvature is conserved (and the sigma increases with <scaleFactor>).[[BR]][[BR]]If specified in conjunction with '-o <outputFileStem>' will also create a curvature file with these values.||
||Scaling||-d||<minCurvature>||-d minCurvature -e maxCurvature[[BR]]Must be used together. (Note to RP: If both args are required, why not make this a single flag with two args? --GW)[[BR]][[BR]]Scale curvature values between <minCurvature> and <maxCurvature>. If the minimum curvature is greater than the maximum curvature, or if either is unspecified, these flags are ignored.[[BR]][[BR]]This scale computation takes precedence over '-c' scaling. [[BR]][[BR]]Note also that the final scaling bounds might not correspond to <minCurvature>... <maxCurvature> since values are scaled across this range so as to preserve the original mean profile.[[BR]][[BR]]If specified in conjunction with '-o <outputFileStem>' will also create a curvature file with these values.||
||Scaling||-e||<maxCurvature>||see -d||
||Scaling||--postScale||<postScale>||Set post scale factor to <postScale>||
||Histogram||-b||<binSize>||Option modifies -h/-p behavior. See ''Histogram details''.||
||Histogram||-i||<binStartCurvature>||Option modifies -h/-p behavior. See ''Histogram details''.||
||Histogram||-j||<binEndCurvature>||Option modifies -h/-p behavior. See ''Histogram details''.||
||Histogram||-p||<numberOfBins>||Same as -h, but use percentage.||
||Filters||--highPassFilter||<highPassFilter>||Set rectified high pass filter to <highPassFilter>. See ''About filters''.||
||Filters||--highPassFilterGaussian||<highPassFilterGaussian>||Set rectified high pass Gaussian filter to <highPassFilterGaussian>. See ''About filters''.||
||Filters||--lowPassFilter||<lowPassFilter>||Set rectified low pass filter to <lowPassFilter>. See ''About filters''.||
||Filters||--lowPassFilterGaussian||<lowPassFilterGaussian>||Set rectified low pass Gaussian filter to <lowPassFilterGaussian>. See ''About filters''.||
||Utility||-h||<numberOfBins>||If -h alone, print usage (''help'') info.[[BR]][[BR]]If specified with argument, prepare a histogram over the range of curvature values, using <numberOfBins> buckets. These are dumped to stdout. See details below under ''Histogram details''. See also -p for percentage version.||
||Utility||-u[[BR]]-?||||Print usage information.||
||Utility||-V[[BR]]-version||||Print out version number.||
||Advanced||-q||<maxUlps>||The <maxUlps> is used to toggle (enable? -- GW) a more rigorous floating point comparison operation in the histogram function. Comparing float values for sorting into bins can at times fail due to number precision issues. If, over the range of comparison some curvature values are not sorted, add <maxUlps>.[[BR]][[BR]]This adds extra function calls to AlmostEqual2sComplement(..) for float comparisons and improves the general accuracy, at a very slight performance penalty.[[BR]][[BR]]You will most likely never have to use this argument, and is for advanced use only.||
||Advanced||-z||<vertexIndex>||Sets the curvature values at that index to zero. The 'raw' curvature, as well as the Gaussian and Mean curvatures are set to zero, and min/max values are recomputed.[[BR]][[BR]]This is useful in cases when outliers in the data (particularly evident in Gaussian calcuations) skew mean and sigma values.||
||Category||Flag|| Arguments ||Description ||
||Basic options||-a|| <numberOfAverages> ||Average the curvature <numberOfAverages> times.||
||Basic options||-f|| <surf_name> ||Set surface (used to calculate curvature) to <surf_name>. Eg: wm, pial etc.||
||Basic options||-g|| ||Calculate Gaussian and Mean||
||Basic options||-l|| <labelFileName> ||(-L) Constrain statistics to the region defined in <labelFileName>.||
||Basic options||-n|| ||Normalise the curvature before computation. Normalisation takes precedence over scaling, so if '-n' is specified in conjunction with '-c' or '-smin'/'-smax' it will override the effects of the scaling.[[BR]]If specified in conjunction with '-o outputFileStem>' will also create a curvature file with these values.||
||Output||-m|| ||Output min / max information for the processed curvature.||
||Output||-o|| <outputFileStem> ||Specifies what files to output and how to name them. This includes condensed text output, histogram files (MatLAB friendly) and curvature files. See details below under ''Output Files'' heading.||
||Output||-s|| <summaryCondition> ||Write out stats as <summaryCondition>. (Not sure what this does -- GW)||
||Output||--writeCurvatureFiles|| ||Toggle (set? --GW) save flag on curvature files||
||Scaling||-c|| <scaleFactor> ||Scale curvature values with <factor>. The mean of the original curvature is conserved (and the sigma increases with <scaleFactor>).[[BR]][[BR]]If specified in conjunction with '-o <outputFileStem>' will also create a curvature file with these values.||
||Scaling||-d|| <minCurvature> ||-d minCurvature -e maxCurvature[[BR]]Must be used together. (Note to RP: If both args are required, why not make this a single flag with two args? --GW)[[BR]][[BR]]Scale curvature values between <minCurvature> and <maxCurvature>. If the minimum curvature is greater than the maximum curvature, or if either is unspecified, these flags are ignored.[[BR]][[BR]]This scale computation takes precedence over '-c' scaling. [[BR]][[BR]]Note also that the final scaling bounds might not correspond to <minCurvature>... <maxCurvature> since values are scaled across this range so as to preserve the original mean profile.[[BR]][[BR]]If specified in conjunction with '-o <outputFileStem>' will also create a curvature file with these values.||
||Scaling||-e|| <maxCurvature> ||see -d||
||Scaling||--postScale|| <postScale> ||Set post scale factor to <postScale>||
||Histogram||-b|| <binSize> ||Option modifies -h/-p behavior. See ''Histogram details''.||
||Histogram||-i|| <binStartCurvature> ||Option modifies -h/-p behavior. See ''Histogram details''.||
||Histogram||-j|| <binEndCurvature> ||Option modifies -h/-p behavior. See ''Histogram details''.||
||Histogram||-p|| <numberOfBins> ||Same as -h, but use percentage.||
||Filters||--highPassFilter|| <highPassFilter> ||Set rectified high pass filter to <highPassFilter>. See ''About filters''.||
||Filters||--highPassFilterGaussian|| <highPassFilterGaussian> ||Set rectified high pass Gaussian filter to <highPassFilterGaussian>. See ''About filters''.||
||Filters||--lowPassFilter|| <lowPassFilter> ||Set rectified low pass filter to <lowPassFilter>. See ''About filters''.||
||Filters||--lowPassFilterGaussian|| <lowPassFilterGaussian> ||Set rectified low pass Gaussian filter to <lowPassFilterGaussian>. See ''About filters''.||
||Utility||-h|| <numberOfBins> ||If -h alone, print usage (''help'') info.[[BR]][[BR]]If specified with argument, prepare a histogram over the range of curvature values, using <numberOfBins> buckets. These are dumped to stdout. See details below under ''Histogram details''. See also -p for percentage version.||
||Utility||-u[[BR]]-?|| ||Print usage information.||
||Utility||-V[[BR]]-version|| ||Print out version number.||
||Advanced||-q|| <maxUlps> ||The <maxUlps> is used to toggle (enable? -- GW) a more rigorous floating point comparison operation in the histogram function. Comparing float values for sorting into bins can at times fail due to number precision issues. If, over the range of comparison some curvature values are not sorted, add <maxUlps>.[[BR]][[BR]]This adds extra function calls to AlmostEqual2sComplement(..) for float comparisons and improves the general accuracy, at a very slight performance penalty.[[BR]][[BR]]You will most likely never have to use this argument, and is for advanced use only.||
||Advanced||-z|| <vertexIndex> ||Sets the curvature values at that index to zero. The 'raw' curvature, as well as the Gaussian and Mean curvatures are set to zero, and min/max values are recomputed.[[BR]][[BR]]This is useful in cases when outliers in the data (particularly evident in Gaussian calcuations) skew mean and sigma values.||

Index TableOfContents

Name

mris_curvature_stats - will primarily compute the mean and variances for a curvature file (or a set of curvature files). These files can be possibly constrained by a label.

Additionally, 'mris_curvature_stats' can report the max/min curvature values, and compute a simple histogram based on these vales.

Curvatures can also be normalised and constrained to a given range before computation.

Gaussian and mean calculations on a surface structure can be performed.

Finally, all output to the console, as well as any new curvatures that result from the above calculations can be saved to a series of text and binary-curvature files. Please see the descriptions of options for more details.

Synopsis

mris_curvature_stats [options] <subjectId> <hemi> <curvFile1> [... <curvFileN]

Arguments

Positional Arguments

subjectId

Subject Id

detailed description (eg, help file information)

hemi

hemisphere

rh or lh

curvFile1..curvFileN

List of one or more existing curvature files to input

Note that this program can also calculate (and save) other curvatures from surfaces selected by other options.

Required Flagged Arguments

Not sure if any flagged arguments are actually required. -- GW

Optional Flagged Arguments

Category

Flag

Arguments

Description

Basic options

-a

<numberOfAverages>

Average the curvature <numberOfAverages> times.

Basic options

-f

<surf_name>

Set surface (used to calculate curvature) to <surf_name>. Eg: wm, pial etc.

Basic options

-g

Calculate Gaussian and Mean

Basic options

-l

<labelFileName>

(-L) Constrain statistics to the region defined in <labelFileName>.

Basic options

-n

Normalise the curvature before computation. Normalisation takes precedence over scaling, so if '-n' is specified in conjunction with '-c' or '-smin'/'-smax' it will override the effects of the scaling.BRIf specified in conjunction with '-o outputFileStem>' will also create a curvature file with these values.

Output

-m

Output min / max information for the processed curvature.

Output

-o

<outputFileStem>

Specifies what files to output and how to name them. This includes condensed text output, histogram files (MatLAB friendly) and curvature files. See details below under Output Files heading.

Output

-s

<summaryCondition>

Write out stats as <summaryCondition>. (Not sure what this does -- GW)

Output

--writeCurvatureFiles

Toggle (set? --GW) save flag on curvature files

Scaling

-c

<scaleFactor>

Scale curvature values with <factor>. The mean of the original curvature is conserved (and the sigma increases with <scaleFactor>).BRBRIf specified in conjunction with '-o <outputFileStem>' will also create a curvature file with these values.

Scaling

-d

<minCurvature>

-d minCurvature -e maxCurvatureBRMust be used together. (Note to RP: If both args are required, why not make this a single flag with two args? --GW)BRBRScale curvature values between <minCurvature> and <maxCurvature>. If the minimum curvature is greater than the maximum curvature, or if either is unspecified, these flags are ignored.BRBRThis scale computation takes precedence over '-c' scaling. BRBRNote also that the final scaling bounds might not correspond to <minCurvature>... <maxCurvature> since values are scaled across this range so as to preserve the original mean profile.BRBRIf specified in conjunction with '-o <outputFileStem>' will also create a curvature file with these values.

Scaling

-e

<maxCurvature>

see -d

Scaling

--postScale

<postScale>

Set post scale factor to <postScale>

Histogram

-b

<binSize>

Option modifies -h/-p behavior. See Histogram details.

Histogram

-i

<binStartCurvature>

Option modifies -h/-p behavior. See Histogram details.

Histogram

-j

<binEndCurvature>

Option modifies -h/-p behavior. See Histogram details.

Histogram

-p

<numberOfBins>

Same as -h, but use percentage.

Filters

--highPassFilter

<highPassFilter>

Set rectified high pass filter to <highPassFilter>. See About filters.

Filters

--highPassFilterGaussian

<highPassFilterGaussian>

Set rectified high pass Gaussian filter to <highPassFilterGaussian>. See About filters.

Filters

--lowPassFilter

<lowPassFilter>

Set rectified low pass filter to <lowPassFilter>. See About filters.

Filters

--lowPassFilterGaussian

<lowPassFilterGaussian>

Set rectified low pass Gaussian filter to <lowPassFilterGaussian>. See About filters.

Utility

-h

<numberOfBins>

If -h alone, print usage (help) info.BRBRIf specified with argument, prepare a histogram over the range of curvature values, using <numberOfBins> buckets. These are dumped to stdout. See details below under Histogram details. See also -p for percentage version.

Utility

-uBR-?

Print usage information.

Utility

-VBR-version

Print out version number.

Advanced

-q

<maxUlps>

The <maxUlps> is used to toggle (enable? -- GW) a more rigorous floating point comparison operation in the histogram function. Comparing float values for sorting into bins can at times fail due to number precision issues. If, over the range of comparison some curvature values are not sorted, add <maxUlps>.BRBRThis adds extra function calls to AlmostEqual2sComplement(..) for float comparisons and improves the general accuracy, at a very slight performance penalty.BRBRYou will most likely never have to use this argument, and is for advanced use only.

Advanced

-z

<vertexIndex>

Sets the curvature values at that index to zero. The 'raw' curvature, as well as the Gaussian and Mean curvatures are set to zero, and min/max values are recomputed.BRBRThis is useful in cases when outliers in the data (particularly evident in Gaussian calcuations) skew mean and sigma values.

Outputs

volume1

description

volume2

description

Description

description

Examples

Example 1

command foo -i f -o out

description

Example 2

command foo -i f -o out -f fvalue

description

Bugs

None

See Also

["othercommand1"], ["othercommand2"]

Links

FreeSurfer

Methods Description

description
description

References

["References/Lastname###"]

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

Author/s

GrahamWideman (Program author: RudolphPienaar)

mris_curvature_stats (last edited 2008-04-29 11:45:53 by localhost)