1,720,961 research outputs found
nibabel 1.0.2
No full text<ul>
<li>Bugfix release</li>
<li>Make inference of data type more robust to changes in numpy dtype hashing</li>
<li>Fix incorrect thresholds in quaternion calculation (thanks to Yarik H for pointing this one out)</li>
<li>Make parrec2nii pass over errors more gracefully</li>
<li>More explicit checks for missing or None field in trackvis and other classes - thanks to Marc-Alexandre Cote</li>
<li>Make logging and error level work as expected - thanks to Yarik H</li>
<li>Loading an image does not change qform or sform - thanks to Yarik H</li>
<li>Allow 0 for nifti scaling as for spec - thanks to Yarik H</li>
<li>nifti1.save now correctly saves single or pair images</li>
</ul>
nibabel 1.1.0
No full text<p>Special thanks to Chris Burns, Jarrod Millman and Yaroslav Halchenko.</p>
<ul>
<li>New feature release</li>
<li>Python 3.2 support</li>
<li>Substantially enhanced gifti reading support (SG)</li>
<li>Refactoring of trackvis read / write to allow reading and writing of voxel
points and mm points in tracks. Deprecate use of negative voxel sizes;
set voxel_order field in trackvis header. Thanks to Chris Filo
Gorgolewski for pointing out the problem and Ruopeng Wang in the trackvis
forum for clarifying the coordinate system of trackvis files.</li>
<li>Added routine to give approximate array orientation in form such as 'RAS'
or 'LPS'</li>
<li>Fix numpy dtype hash errors for numpy 1.2.1</li>
<li>Other bug fixes as for 1.0.2</li>
</ul>
nibabel 1.2.1
No full text<p>Particular thanks to Yaroslav Halchecko for fixes and cleanups in this
release.</p>
<ul>
<li>Bugfix release</li>
<li>Make compatible with pydicom 0.9.7</li>
<li>Refactor, rename nifti diagnostic script to nib-nifti-dx
</li>
<li>Fix a bug causing an error when analyzing affines for orientation, when the
affine contained all 0 columns</li>
<li>Add missing dicomfs script to installation list and rename to
nib-dicomfs
</li>
</ul>
nibabel 1.2.1
No full text<p>Particular thanks to Yaroslav Halchecko for fixes and cleanups in this release.</p>
<ul>
<li>Bugfix release</li>
<li>Make compatible with pydicom 0.9.7</li>
<li>Refactor, rename nifti diagnostic script to nib-nifti-dx</li>
<li>Fix a bug causing an error when analyzing affines for orientation, when the affine contained all 0 columns</li>
<li>Add missing dicomfs script to installation list and rename to nib-dicomfs</li>
</ul>
nibabel 1.2.0
No full text<p>This release had large contributions from Krish Subramaniam, Alexandre Gramfort, Cindee Madison, Félix C. Morency and Christian Haselgrove.</p>
<ul>
<li>New feature and bugfix release</li>
<li>Freesurfer format support by Krish Subramaniam and Alexandre Gramfort.</li>
<li>ECAT read write support by Cindee Madison and Félix C. Morency.</li>
<li>A DICOM fuse filesystem by Christian Haselgrove.</li>
<li>Much work on making data scaling on read and write more robust to rounding error and overflow (MB).</li>
<li>Import of nipy functions for working with affine transformation matrices.</li>
<li>Added methods for working with nifti sform and qform fields by Bago Amirbekian and MB, with useful discussion by Brendan Moloney.</li>
<li>Fixes to read / write of RGB analyze images by Bago Amirbekian.</li>
<li>Extensions to concat_images by Yannick Schwartz.</li>
<li>A new nib-ls script to display information about neuroimaging files, and various other useful fixes by Yaroslav Halchenko.</li>
</ul>
nibabel 2.0.0
No full text<p>This release had large contributions from Eric Larson, Brendan Moloney,
Nolan Nichols, Basile Pinsard, Chris Johnson and Nikolaas N. Oosterhof.</p>
<ul>
<li>New feature, bugfix release with minor API breakage;</li>
<li>Minor API breakage: default write of NIfTI / Analyze image data offset
value. The data offset is the number of bytes from the beginning of file
to skip before reading the image data. Nibabel behavior changed from
keeping the value as read from file, to setting the offset to zero on
read, and setting the offset when writing the header. The value of the
offset will now be the minimum value necessary to make room for the header
and any extensions when writing the file. You can override the default
offset by setting value explicitly to some value other than zero. To read
the original data offset as read from the header, use the offset
property of the image dataobj attribute;</li>
<li>Minor API breakage: data scaling in NIfTI / Analyze now set to NaN when
reading images. Data scaling refers to the data intercept and slope
values in the NIfTI / Analyze header. To read the original data scaling
you need to look at the slope and inter properties of the image
dataobj attribute. You can set scaling explicitly by setting the
slope and intercept values in the header to values other than NaN;</li>
<li>New API for managing image caching; images have an in_memory property
that is true if the image data has been loaded into cache, or is already
an array in memory; get_data has new keyword argument caching to
specify whether the cache should be filled by get_data;</li>
<li>Images now have properties dataobj, affine, header. We will
slowly phase out the get_affine and get_header image methods;</li>
<li>The image dataobj can be sliced using an efficient algorithm to avoid
reading unnecessary data from disk. This makes it possible to do very
efficient reads of single volumes from a time series;</li>
<li>NIfTI2 read / write support;</li>
<li>Read support for MINC2;</li>
<li>Much extended read support for PAR / REC, largely due to work from Eric
Larson and Gregory R. Lee on new code, advice and code review. Thanks also
to Jeff Stevenson and Bennett Landman for helpful discussion;</li>
<li>
parrec2nii script outputs images in LAS voxel orientation, which
appears to be necessary for compatibility with FSL dtifit /
fslview diffusion analysis pipeline;</li>
<li>Preliminary support for Philips multiframe DICOM images (thanks to Nolan
Nichols, Ly Nguyen and Brendan Moloney);</li>
<li>New function to save Freesurfer annotation files (by Github user ohinds);</li>
<li>Method to return MGH format vox2ras_tkr affine (Eric Larson);</li>
<li>A new API for reading unscaled data from NIfTI and other images, using
img.dataobj.get_unscaled(). Deprecate previous way of doing this,
which was to read data with the read_img_data function;</li>
<li>Fix for bug when replacing NaN values with zero when writing floating
point data as integers. If the input floating point data range did not
include zero, then NaN would not get written to a value corresponding to
zero in the output;</li>
<li>Improvements and bug fixes to image orientation calculation and DICOM
wrappers by Brendan Moloney;</li>
<li>Bug fixes writing GIfTI files. We were using a base64 encoding that didn't
match the spec, and the wrong field name for the endian code. Thanks to
Basile Pinsard and Russ Poldrack for diagnosis and fixes;</li>
<li>Bug fix in freesurfer.read_annot with orig_ids=False when annot
contains vertices with no label (Alexandre Gramfort);</li>
<li>More tutorials in the documentation, including introductory tutorial on
DICOM, and on coordinate systems;</li>
<li>Lots of code refactoring, including moving to common code-base for Python
2 and Python 3;</li>
<li>New mechanism to add images for tests via git submodules.</li>
</ul>
nibabel 1.2.2
No full text<ul>
<li>Bugfix release</li>
<li>Fix longdouble tests for Debian PPC (thanks to Yaroslav Halchecko for finding and diagnosing these errors)</li>
<li>Generalize longdouble tests in the hope of making them more robust</li>
<li>Disable saving of float128 nifti type unless platform has real IEEE binary128 longdouble type.</li>
</ul>
nibabel 1.3.0
No full text<p>Special thanks to Chris Johnson, Brendan Moloney and JB Poline.</p>
<ul>
<li>New feature and bugfix release</li>
<li>Add ability to write Freesurfer triangle files (Chris Johnson)</li>
<li>Relax threshold for detecting rank deficient affines in orientation
detection (JB Poline)</li>
<li>Fix for DICOM slice normal numerical error (issue #137) (Brendan Moloney)</li>
<li>Fix for Python 3 error when writing zero bytes for offset padding</li>
</ul>
nibabel 1.0.2
No full text<ul>
<li>Bugfix release</li>
<li>Make inference of data type more robust to changes in numpy dtype hashing</li>
<li>Fix incorrect thresholds in quaternion calculation (thanks to Yarik H for
pointing this one out)</li>
<li>Make parrec2nii pass over errors more gracefully</li>
<li>More explicit checks for missing or None field in trackvis and other
classes - thanks to Marc-Alexandre Cote</li>
<li>Make logging and error level work as expected - thanks to Yarik H</li>
<li>Loading an image does not change qform or sform - thanks to Yarik H</li>
<li>Allow 0 for nifti scaling as for spec - thanks to Yarik H</li>
<li>nifti1.save now correctly saves single or pair images</li>
</ul>
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