Ds105 analysis #1
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Windows raised an error, apparently because of undeleted objects with references to temporary files.
Scripts were using outdated imageformats import, now failing.
ENH: Make it possible to input slice_order=None to FmriRealign4d This should fix issue nipy#228.
BF: fixed bug in resampling for unsigned type images This branch fixes a bug in the resample function from nipy.algorithms.registration, which returns an image with same dtype as the input image, meaning that any interpolated value needs be converted to the closest value according to the dtype. The conversion was not done properly for images encoded in unsigned integer types as negative values (which can arise here and there due to cubic spline interpolation) would be converted using a simple cast in C. This has been fixed by checking dtype.kind and forcing negative values to zero whenever dtype.kind=='u'.
Fix roi glm example This PR solves both issue nipy#224 and a random failure of the example.
…n quantile C-routine
Make single test functions run many tests.
RF: extend quantile and median tests Make single test functions run many tests.
Refactor quantile routine
…cit variable naming
The buildbots build mpkgs; this script builds dmgs from the mpkgs and sets the permissions correctly.
Fetched from the dipy/tools directory.
That I missed somehow.
From comments by Bertrand
We were pointing to the old deprecated function.
The ``screens`` utility assumed time last and slice second-to-last. Get screens to look for 't' axis (will nearly always be last, but often set), or accept suggestion from arguments; ditto for slice axis.
Add tests for slice axis and time axis specified.
This is minor API breakage, because previous default behavior was:
time_axis=-2, slice_axis default -> -2
time_axis=0, slice_axis_default -> -2
Now:
time_axis=-2, slice_axis default -> -1
time_axis=0, slice_axis_default -> -1
Allow nipy_diagnose to work on arbitrary slice axis
DOC: fix a typo: "their is" -> "there is"
NF: add script to build dmg files from buildbots The buildbots build mpkgs; this script builds dmgs from the mpkgs and sets the permissions correctly.
MRG: Fix type graph This PR aims at solving issue nipy#256 by casting to float 64 the arrays that need to. I took this opportunity to clean the tests in nipy.algorithms.graph.
because we're set up properly on nipy.org now.
MRG: Screens refactor I found a dataset that had the slice dimension first (the Haxby 2001 datset, ds105 on OpenFMRI.org). To do slice timing we need to be able to specify the slice dimension. These changes allow you to specify the slice dimension to the utilities for time series differences (which depend on slice).
MRG: Fix bsa
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I've managed to get (what I think is) an appropriate single run model going. For the FIAC data, we had actually used warped fMRI which doesn't seem included in this data, unless I'm mistaken.
Added a block_design function that might be useful for other studies.