WIP: modifying artifact detect to account for head size #464
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Did you figure out what was causing the MultiProc freeze? |
set to agg to ensure multiproc plugin can be used. deprication warning for new flag "bound_by_brainmask"
due to matplotlib backend. only when |
removed Siemens option - was not supported anyway.
* sty: some pep8 cleanup * fix: convert nipy motion parameters to matrix using nipy * api: added option to use particular threshold when creating brain mask internally * enh: save mask used for global signal calculation
* master: Fixed afni test Fixed AFNI tests. Escape the expr parameter in 3dcalc. fixing TSNR integer data bug ENH: Provide access to all relevant BET outputs when "surfaces" option used.
* master: Removed unnecessary usedefault. fixed typo in a file name fix: github authentication Going back to distinguishing affine transformations by names. Improved docs. fixed typo in randomize parameters Removed unnecessary copyfiles and added output_image option. BF: Pass plugin_args to child nodes of MapNode ENH: Don't require ordereddict for python < 2.7 BF: Fix for plugins when using python2.7 Fixed parenthesis. Fix fslreorient2std output collection Allow FNIRT to take standard names as reference. BF: Check plugin_args is not None before accessing it like a dict.
* master: fix: fsl tests sty: white space fix: automask bug when apply_mask is not specified fix: updated test writer with additional metadata fix: remove unnecessary print statement fix: trim http link for code fix: github url generation fix: return full hash
* master: (127 commits) fix: doctest carriage return fix: deprecation warning does not reset trait to Undefined - will set new value add support for template files API fix for somaworkflow PEP8 Further refactoring Reafactoring - less redundant code between SGE and PBS. Respect custom execution parameters in graph based models. Doctest fix, better error reporting. fix: config updated before checking for deprecated options put back the n_procs docs Udated docs with n_procs for MultiProc DOC: Added docstring for MpiCommandLine with example usage. DOC: Improve docstring for DataFinder, include example usage. fix: adding atlases fix: removing recommends fix: restore fsl fix: remove fsl for now fix: variable name fix: use neurodebian sources ...
* master: fix: ants workflows setup deprecated version should be a string, added AFNITraitedSpec for backward compatibility docs PEP8 name_source can be a list, make "infolder" a deprecated name Removed unnecessary outputsspecs Renaming Bugfixes, don't overlad extensions by default. fixed AutoTcorrelate and _list_outputs added skeleton AutoTcorrelate turns out some traits don't have "_metadata" fixed hashing PEP8 added prefix/suffix deprecation info All autogenerated inputs should not be hashed. Refactored AFNI. Added new autogenerating input type. Refactor AFNI added "tar.gz" as a unusual extension graph submission fix
* master: (24 commits) Fix nipy#493 Fixes nipy#459 fixed doctests changelog BF: Fixed several issues with GroupAndStack interface DOC: Various clean up an improvements to docstrings. DOC: Added example to LookupMeta docstring ENH: Allow meta_keys input to LookupMeta be a mapping. minor fixes doc: added version config info to doc enh: added output versioning as well BF: Wrap imports of optional deps in try-except block STY: Cleanup some long lines. ENH: Making interface module name dcmstack to match package ENH: Allow control of meta data filtering in DcmStack. BF: Fixed bug in CopyMeta ENH: Default to 'force=True' when reading DICOM files. BF: CopyMeta inputspec and outputspec were undefined. WIP: Initial interface to dcmstack package. sty: pep8 ...
…ng bounds_by_brainmask
Code cleanup.
chrisgorgo
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Dec 18, 2012
WIP: modifying artifact detect to account for head size
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This is very much a wip. i will continue to add the following features:
save voxel displacement time seriesadd afni support