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Bug #188776: No documentation for mincSum and friends	Undecided	Fix Committed
Bug #192228: mincFDR does not work with imported volumes	Undecided	Fix Committed

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Related blueprints

89. By mcvaneede on 2012-05-22

fixed a bug in mincFDR.mincMultiDim. When calculating the thresholds at the different
significance levels, the if-statement only returned a threshold when there were at
least 2 results, instead of at least 1.

88. By mcvaneede on 2012-05-09

* in the function anatLm, added the attributes "stat-type" and "df" to the output. The output can be used as an argument to anatFDR which requires these attributes.

87. By EJ Nikelski on 2011-01-01

* added a new 'labels' argument to volume.explodeLabelVolume to permit
  specification of a subset of labels that one wants exploded out as
  masks.
* fixed a volume type determination error in mincIO.writeVolumeX.
  Label volumes were not being identified as such due to
  issues relating to use of floating point values to represent
  integers.

86. By EJ Nikelski on 2010-08-14

(1) added a couple of civet convenience functions to
    compute tissue volumes.
(2) added a civet convenience function to compute the
    global native-to-icbm_model rescaling factor. This
    is super useful in creating volume estimates in native
    space, given icbm values as input.
(3) fixed some documentation-related problems that came
    out in R CMD check

85. By EJ Nikelski on 2010-07-28

(1) added a bunch of civet convenience functions. All functions
    are prefixed with civet.*

(2) added renamed versions of both of Jason's civet functions,
    matching the new naming convention. The previous versions
    still exist, but have had deprecation warnings added.

(3) added a new volume.* prefix for functions that do
    non-statistical processing on volumes.

(4) added function volume.explodeLabelVolume() to split, for
    example, a Civet classify volume into its 4 component
    volumes. Also added function volume.combineMaskVolumes()
    to, ummmm, combine any number of mask volume objects into
    a unified mask volume object.

(5) finally got around to figuring out how to overload the
    basic S4 arithmetic operators, allowing me to now do
    "+-*/" operations on MincVolumeIO objects without
    having the resulting objects converted to array objects.

(6) added a new "label" volume type which is auto-detected and
    displayed using a spectral-ish colormap (like the functional
    volumes).

(7) added a new "mask" volume type which is auto-detected and
    displayed using a gray-scale (really just black and white)
    colormap.

84. By EJ Nikelski on 2010-05-13

Changes:
(1) Added "setter" methods for mincIO class S4 objects.
    The method naming follows the "getters", thus we now
    have:
    1. getProperty()
    2. setProperty()

    With the addition of these methods, users can now
    write code without needing to be aware of the underlying
    implementation. The previous state of affairs was quite
    an embarrassment, and now I can walk proudly without
    shame ... or significantly less shame.
(2) Added Rd entry for setters
(3) Modified the mincIO Sweave doc to introduce and show
    use of the setters.

83. By EJ Nikelski on 2010-04-30

Changes:

(1) created a new set of accessor methods for all mincIO objects. This permits the
    users to get access to all mincIO slot values without needing to fiddle with
    or beware of the internal S4 object organization. Yes, it is much better
    this way. BTW, the accessor is called mincIO.getProperty().

(2) updated the mincIO Sweave doc to use the new mincIO.getProperty()
    accessor method.

82. By EJ Nikelski on 2010-04-29

A few assorted changes:

(1) moved all of the S4 generics into a new AllGenerics.R file

(2) incremented the sub-version number by .0.1, since we've actually made
    some fairly extensive changes over the last few commits.

81. By EJ Nikelski on 2010-04-29

These are mostly just fixes to clean up our "R CMD check" output a liitle.
Here's a list of the bits and pieces:

(1) Added the "PACKAGE=" argument to all .C/.Call calls.
    This mostly required specification of the "RMINC" package, however,
    in some of the rmincLmeLoop.R functions, we needed to specify "nlme".
    Note to self: How on earth is the nlme library loaded? Not loaded with
    RMINC, and no explicit load command that I could see. Does this stuff
    even work?

(2) Added an "\VignetteIndexEntry" line to all Sweave docs

(3) Added all undocumented functions to the RMINC-internal.Rd file.
    If anyone ever gets bored ... or if we want to release this package for general
    usage, most of the functions contained here will need a doc page be written.

(4) Fixed some mincIO S4 signatures and related documentation.

(5) Substituted all logical "T/F" with "TRUE/FALSE". While the T/F form works, it's neither
    recommended not supported. CMD check winges about it.

(6) Loads of fixes to classical RMINC functions and S3 methods.

80. By EJ Nikelski on 2010-04-22

Added a prefix to all mincIO methods and functions. In particular, all functions
dealing directly with mincIO objects now sport a mincIO.* prefix, common functions
that are not mincIO-specific, now have a rminc.* prefix. Why the prefix? Well,

(1) Jason seemed to be moving in this direction anyway
(2) it makes what is slowly becoming a very large package somewhat more manageable
(3) I found that using the prefix makes it easier to use Tab-completion when writing
    code in an editor that supports this ... as well as the R command line. It's
    quite lovely to be able to type "mincIO.<tab>" and see a list of all mincIO
    methods/functions. Yes, I know that Jason was trying to move away from using
    the "." as a delimiter within function names due to the goofy way that S3 method
    scheduling works ... but
    (a) none of these functions are S3
    (b) this way looks so purdy.