Release Name: 0.2.9
Notes:
This is a minor release, with the main changes being the following:
- added overlay feature to MRView
- fix some issues in handling of GE DICOM data
- performance improvements for tracks2prob
Changes:
=======================================================================
VERSION 0.2.9
=======================================================================
24-08-2010 Robert Smith <r.smith@brain.org.au>
* cmd/tracks2prob.cpp:
fix bug in handling of multiple contributions to a single voxel from a single track
04-08-2010 Robert Smith <r.smith@brain.org.au>
* cmd/tracks2prob.cpp:
reverted to previous interpretation of track 'density'
(no scaling factor, finer interpolation & unary track->voxel contribution)
* lib/point.h:
added const qualifier to declaration of member function Point::cross()
28-07-2010 J-Donald Tournier <d.tournier@brain.org.au>
* src/mrview/sidebar/tractography/track_list_item.h:
increased allocator slab size to 32MB to force release of RAM to OS on close()
* doc/faq.html:
add entry about issues with the Analyse image format
* doc/install/unix.html:
remove obsolote installation instructions for 64 bit systems
* sysconf/linux.py:
switch '-march' option to 'native' to allow compilation on 64-bit systems
without manual editing (suggested by Rob Smith).
21-07-2010 J-Donald Tournier <d.tournier@brain.org.au>
* src/dwi/SH.h:
* src/dwi/SH.cpp:
improved SH::delta() function
* src/mrview/sidebar/overlay.h:
* src/mrview/sidebar/overlay.cpp:
* src/mrview/sidebar/main.h:
* src/mrview/sidebar/main.cpp:
added new overlay sidebar tool
16-07-2010 J-Donald Tournier <d.tournier@brain.org.au>
* lib/file/dicom/image.cpp:
check for readable data in GE private DW tags before assigning
* lib/file/dicom/element.cpp:
fix bug in handling of big-endian files
15-07-2010 J-Donald Tournier <d.tournier@brain.org.au>
* build:
fix to allow the use of symbolic links (problem identified by Rob
Smith)
* Doxyfile: version number upped to 0.2.9
* lib/mrtrix.h: MRTRIX_MICRO_VERSION upped to 9
14-07-2010 Robert Smith <r.smith@brain.org.au>
* cmd/tracks2prob.cpp:
major overhaul of tracks2prob
=======================================================================
VERSION 0.2.8
=======================================================================
15-03-2010 J-Donald Tournier <d.tournier@brain.org.au>
* lib/mrtrix.h:
* lib/file/dicom/tree.cpp:
add shorten() function to reduce long filenames
12-03-2010 J-Donald Tournier <d.tournier@brain.org.au>
* src/mrview/sidebar/tractography/track_list.h:
* src/mrview/sidebar/tractography/track_list.cpp:
* src/mrview/sidebar/tractography/track_list_item.h:
* src/mrview/sidebar/tractography/track_list_item.cpp:
a few bug fixes for the colour handling and support for depth blend on
64 bit systems
04-03-2010 J-Donald Tournier <d.tournier@brain.org.au>
* src/mrview/scaling.h:
fix automatic windowing in the presence of infinite or NaN voxel values.
03-03-2010 J-Donald Tournier <d.tournier@brain.org.au>
* cmd/normalise_tracks.cpp:
skip points in the tracks file if they are outside the supplied warp
* cmd/streamtrack.cpp:
* src/dwi/tractography/tracker/base.h:
* src/dwi/tractography/tracker/base.cpp:
new option to stop tracking as soon as track enters any include region.
* cmd/streamtrack.cpp:
* src/dwi/tractography/tracker/base.h:
* src/dwi/tractography/tracker/base.cpp:
new option to prevent tri-linear interpolation of mask regions.
* src/dwi/tractography/tracker/base.h:
* src/dwi/tractography/tracker/base.cpp:
* src/dwi/tractography/tracker/dt_stream.cpp:
* src/dwi/tractography/tracker/sd_stream.cpp:
* src/dwi/tractography/tracker/sd_prob.cpp:
tracking now stops immediately before the track leaves the mask, rather
than immediately after.
* lib/file/dicom/image.h:
* lib/file/dicom/image.cpp:
* lib/file/dicom/mapper.cpp:
improved GE gradient information support
* lib/file/dicom/element.cpp: fix bug in handling of IS sequences
09-12-2009 J-Donald Tournier <d.tournier@brain.org.au>
* lib/file/dicom/mapper.cpp: handle zero directions in gradient scheme
* lib/file/dicom/image.cpp: preliminary GE gradient information support
02-12-2009 J-Donald Tournier <d.tournier@brain.org.au>
* lib/file/key_value.cpp: minor bug that prevented reading read-only files
27-11-2009 J-Donald Tournier <d.tournier@brain.org.au>
* src/mrview/pane.cpp:
* src/dwi/render_frame.cpp:
minor change to receive mouse move events on newer linux distributions (e.g. Ubuntu Karmic)
04-11-2009 J-Donald Tournier <d.tournier@brain.org.au>
* cmd/average.cpp: fix -axis option
29-10-2008 J-Donald Tournier <d.tournier@brain.org.au>
* cmd/mrabs.cpp: new command to take absolute value of image intensities
14-10-2009 J-Donald Tournier <d.tournier@brain.org.au>
* lib/mrtrix.cpp: fix parse_float() to handle NaN in string specification
13-10-2009 J-Donald Tournier <d.tournier@brain.org.au>
* cmd/streamtrack.cpp:
- clarified the meaning of command-line options "number" & "maxnum"
- fixed incorrect default setting of "maxnum" value
25-09-2009 J-Donald Tournier <d.tournier@brain.org.au>
* cmd/dwi2SH.cpp:
* cmd/csdeconv.cpp:
* cmd/sdeconv.cpp: fix documentation of SH coefficient storage convention
22-09-2009 J-Donald Tournier <d.tournier@brain.org.au>
* src/mrview/sidebar/orientation_plot.cpp: add config option to set background colour
17-09-2009 J-Donald Tournier <d.tournier@brain.org.au>
* cmd/dwi2tensor.cpp: improved support for images that might use a different dimension for the DWI
17-09-2009 J-Donald Tournier <d.tournier@brain.org.au>
* lib/file/dicom/image.cpp: added preliminary support to read Philips DW information
17-09-2009 J-Donald Tournier <d.tournier@brain.org.au>
* lib/app.cpp: fix bug in command-line parsing (fix supplied by Tom Close)
11-09-2009 J-Donald Tournier <d.tournier@brain.org.au>
* src/dwi/SH.cpp: fix bug in computation of second derivative of SH series (pointed out by Ben Jeurissen).
09-09-2009 J-Donald Tournier <d.tournier@brain.org.au>
* lib/file/dicom/csa_entry.h:
* lib/file/dicom/element.cpp:
include <cstdio> to allow compilation on Fedora 11
=======================================================================
VERSION 0.2.7
=======================================================================
24-08-2009 J-Donald Tournier <d.tournier@brain.org.au>
* src/dwi/tensor.h: use sqrt(1.5) instead of sqrt(3/2) when computing the
FA. This was rounded down to 1 since the compiler assumed integer
arithmetic (thanks to Kerstin Pannek for pointing this out).
16-08-2009 J-Donald Tournier <d.tournier@brain.org.au>
* cmd/resample_tracks.cpp: Improved the track resampling routine to allow for curved tracks.
13-08-2009 J-Donald Tournier <d.tournier@brain.org.au>
* cmd/gen_unit_warp.cpp: Added command to generate unitary warp. This is
intended for use with other normalisation programs. The unitary warp field
generated by this program can be warped by a third party normalisation
routine, so that the relevant warp field can be recovered in the right
format for use with MRtrix.
* cmd/gen_ROI.cpp:
* cmd/resample_tracks.cpp:
* cmd/sample_tracks.cpp: Added a few programs to perform track-specific analyses
23-07-2009 J-Donald Tournier <d.tournier@brain.org.au>
* lib/image/format/nifti1.cpp: Fix bitwise read handling for NIfTI format
26-06-2009 J-Donald Tournier <d.tournier@brain.org.au>
* cmd/streamtrack.cpp: added "maxnum" option to limit the number of tracks attempted
10-06-2009 J-Donald Tournier <d.tournier@brain.org.au>
* lib/file/dicom/image.cpp: fix handling of acquisition matrix when the rows & columns are interchanged.
27-05-2009 J-Donald Tournier <d.tournier@brain.org.au>
* cmd/mrstats.cpp: added option to dump voxel intensities into a text file
20-05-2009 J-Donald Tournier <d.tournier@brain.org.au>
* cmd/mrstats.cpp: added option to build intensity histogram
19-05-2009 J-Donald Tournier <d.tournier@brain.org.au>
* cmd/csdeconv.cpp: fix incorrect setting of the threshold option - it was set
to a value 100 times lower than specified (reported by Ben Jeurissen).
18-05-2009 J-Donald Tournier <d.tournier@brain.org.au>
* cmd/threshold.cpp: reset scale & offset of output image to ensure proper binary output
01-05-2009 J-Donald Tournier <d.tournier@brain.org.au>
* src/dwi/tractography/file.cpp: fix minor bug that caused first point of
first track to be omitted (reported by Tom Close).
01-04-2009 J-Donald Tournier <d.tournier@brain.org.au>
* cmd/normalise_tracks.cpp: added command to apply normalisation transform to tracks.
=======================================================================
VERSION 0.2.6
=======================================================================
21-03-2009 J-Donald Tournier <d.tournier@brain.org.au>
* cmd/streamtrack.cpp: fix minor bug that caused tracking to hang on 64-bit machines
18-03-2009 J-Donald Tournier <d.tournier@brain.org.au>
* src/dwi/tractography/tracker/base.h:
* src/dwi/tractography/tracker/base.cpp:
fix serious bug that caused the tracking to be incorrect with obliquely aligned data sets
17-03-2009 J-Donald Tournier <d.tournier@brain.org.au>
* lib/file/dicom/element.h:
* lib/file/dicom/element.cpp:
modify to allow use of either TR1 unordered map or SGI hash_map for the DICOM dictionary
* lib/hash_map.h: Use the C++ TR1 unordered_map instead of hash_map by default
This avoids compilation warnings on newer compilers. The old SGI hash_map can be used by removing
the USE_TR1 macro on the command-line (i.e. remove the '-DUSE_TR1' entry in the cpp_flags
line of the relevant sysconf file).
* lib/image/header.cpp: additional sanity checks in sanitise_transform():
- make sure voxel sizes are finite numbers
- make sure all entries in the transform matrix are finite.
use sane defaults otherwise.
19-12-2008 J-Donald Tournier <d.tournier@brain.org.au>
* lib/file/dicom/mapper.cpp: handle cases where the data size is greater than expected,
and interpret as multi-channel data.
* lib/file/dicom/quick_scan.h:
* lib/file/dicom/quick_scan.cpp:
* lib/file/dicom/tree.cpp: various sanity checks to ignore non-image DICOM files
18-12-2008 J-Donald Tournier <d.tournier@brain.org.au>
* lib/image/format/dicom.cpp: handle cases where no series have been selected
* lib/file/dicom/element.cpp: printout of DICOM group & element is now in hexadecimal
* lib/file/dicom/select_cmdline.cpp: change numbering of series to handle cases where the series number is not set
* src/mrview/image.cpp: fix random crashes in MRView when the "View->snap to image axes" option is unticked.
* src/dwi/SH.cpp: modify precomputation to allow thread-safe operation
* src/dwi/tractography/tracker/dt_stream.h:
* src/dwi/tractography/tracker/dt_stream.cpp: modify eigenvector computation to allow thread-safe operation
* cmd/streamtrack.cpp: added multithreading capability
17-12-2008 J-Donald Tournier <d.tournier@brain.org.au>
* cmd/mrstats.cpp: new command to compute voxelwise statistics
* cmd/tensor_metrics.cpp: new command to compute various tensor-derived metrics
* src/dwi/tensor.h: minor changes to tidy up the code
15-12-2008 J-Donald Tournier <d.tournier@brain.org.au>
* src/mrview/sidebar/tractography/track_list_item.h:
* src/mrview/sidebar/tractography/track_list_item.cpp:
* src/mrview/sidebar/tractography/track_list.h:
* src/mrview/sidebar/tractography/track_list.cpp:
a few bug fixes + memory performance improvements for the depth blend option
12-12-2008 J-Donald Tournier <d.tournier@brain.org.au>
* src/mrview/sidebar/screen_capture.h:
* src/mrview/sidebar/screen_capture.cpp:
new sidebar tool for taking screenshots in MRView
01-12-2008 J-Donald Tournier <d.tournier@brain.org.au>
* src/mrview/sidebar/orientation_plot.cpp: fix problems with invalid focus position when the tool is first initialised.
31-10-2008 J-Donald Tournier <d.tournier@brain.org.au>
* lib/mrtrix.h: include <cstring> & <cstdlib> to allow compilation on Fedora 9
* cmd/sdeconv.cpp:
* cmd/csdeconv.cpp:
use MR::Ptr instead of std::auto_ptr
* cmd/mrinfo.cpp: remove obsolete -dicom & -csa options
* lib/file/dicom/element.cpp: only attempt to read a "truncated format" DICOM file if the extension is ".dcm"
* lib/get_set.h:
- replace get::T and put::T() methods with template get<T>() & put<T>() methods
- add get/put template specialisations for bool, int8 and uint8
- remove obsolete ArrayXX classes
- move MR::ByteOrder namespace & methods from lib/mrtrix.h to here
* lib/image/mapper.cpp: use template get<T>() & put<T>() methods from lib/get_set.h
* cmd/tracks2prob.cpp: various optimisations to improve performance
* lib/file/dicom/mapper.cpp: scale b-value by gradient magnitude and normalise gradient direction
29-10-2008 J-Donald Tournier <d.tournier@brain.org.au>
* src/dwi/SH.cpp: fix precomputed value calculation to handle rounding errors in the angle
* cmd/streamtrack.cpp:
* src/dwi/tractography/tracker/base.h:
* src/dwi/tractography/tracker/base.cpp:
fix init_direction handling
24-10-2008 J-Donald Tournier <d.tournier@brain.org.au>
* cmd/disp_profile.cpp: various improvements
- set lmax based on SH values provided
- set title based on row of SH coefficients currently displayed
- use shift modifier to scroll through 10 rows at a time
- add menu entry to normalise plot amplitude
* src/dwi/render_frame.h: add functions to normalise plot amplitude
* src/dwi/render_frame.cpp: scale plot by SH(0,0) coefficient when normalise option is set
17-10-2008 J-Donald Tournier <d.tournier@brain.org.au>
* build: update script to allow use with separate projects
* lib/app.h: add SET_VERSION_DEFAULT, SET_VERSION, SET_AUTHOR and SET_COPYRIGHT macros
* lib/app.cpp: modify version information printed out by "-version" option
to take account of new command version, copyright and author variables
* cmd/disp_profile.cpp: add option -response to display response function
15-10-2008 J-Donald Tournier <d.tournier@brain.org.au>
* cmd/mrconvert.cpp: add -layout option to manipulate data ordering within the image file
* cmd/mrconvert.cpp: fix -prs option handling
* cmd/mrconvert.cpp:
* lib/file/dicom/mapper.h:
* lib/file/dicom/mapper.cpp:
* lib/image/format/dicom.cpp:
* src/dialog/file.cpp:
remove MR::DICOM_DW_gradients_PRS flag
03-10-2008 J-Donald Tournier <d.tournier@brain.org.au>
* cmd/find_SH_peaks.cpp: fix bug in looping structure to allow processing of whole data set.
02-10-2008 J-Donald Tournier <d.tournier@brain.org.au>
* lib/mrtrix.h: change Exception silencing to a priority level changing approach
02-10-2008 J-Donald Tournier <d.tournier@brain.org.au>
* lib/file/dicom/element.cpp: extra sanity check to make sure that each element fits within the file.
01-10-2008 J-Donald Tournier <d.tournier@brain.org.au>
* lib/image/object.cpp: sanitise axes prior to creating an image
* lib/image/axis.h: added sanitise() method to correct inconsistent axes ordering
23-09-2008 J-Donald Tournier <d.tournier@brain.org.au>
* lib/file/dicom/csa_entry.h: fix handling of ascii floating-point numbers
on locales that use a comma as the decimal separator.
15-09-2008 J-Donald Tournier <d.tournier@brain.org.au>
* lib/file/dicom/quickscan.cpp:
* lib/file/dicom/tree.cpp:
* lib/file/dicom/patient.cpp:
* lib/file/dicom/study.cpp:
handle files even when any of the study, series or patient description fields are blank
08-09-2008 J-Donald Tournier <d.tournier@brain.org.au>
* lib/file/dicom/image.h,
* lib/file/dicom/image.cpp,
* lib/file/dicom/mapper.cpp:
fix handling of mosaic slice ordering (using SliceNormalVector entry in CSA header)
* Doxyfile: version number upped to 0.2.6
* lib/mrtrix.h: MRTRIX_MICRO_VERSION upped to 6
=======================================================================
VERSION 0.2.5
=======================================================================
23-09-2008 J-Donald Tournier <d.tournier@brain.org.au>
* lib/file/dicom/csa_entry.h: fix handling of ascii floating-point numbers on locales
that use a comma as the decimal separator.
03-09-2008 J-Donald Tournier <d.tournier@brain.org.au>
* doc: a number of updates
- new FAQ section
- document NIfTI format
- other minor updates
02-09-2008 J-Donald Tournier <d.tournier@brain.org.au>
* lib/image/format/mrtrix.cpp: add capacity to create temporary files for use through pipes
* lib/mrtrix.h: added is_temporary() method to identify temporary files
* lib/image/format/mri.cpp: remove temporary file creation capacity
* lib/image/object.cpp: update temporary file handling (i.e. those sent via pipes)
- switch to MRtrix format as the standard format for temporary files
- handle any type of image supplied through the standard input
* lib/file/mmap.h: tidied up class structure (MMap::Base is now private to MMap)
* src/dwi/tractography/tracker/base.h: handle rare cases where gen_seed() would fail
* lib/image/format/analyse.cpp: add support for reading NIfTI-1.1 hdr/img pairs
29-08-2008 J-Donald Tournier <d.tournier@brain.org.au>
* lib/image/object.cpp: in create(), finalise the byte order after the handler's check() method
to allow different file formats to override the data type more easily.
* cmd/mrtransform.cpp: new command to re-orient or reslice images (needed
to apply transforms supplied by FSL's FLIRT command).
27-08-2008 J-Donald Tournier <d.tournier@brain.org.au>
* lib/image/format/nifti1.cpp: support for reading/writing NIfTI-1.1 *.nii files
* Doxyfile: version number upped to 0.2.5
* lib/mrtrix.h: MRTRIX_MICRO_VERSION upped to 5
=======================================================================
VERSION 0.2.4
=======================================================================
04-08-2008 J-Donald Tournier <d.tournier@brain.org.au>
* doc/install/unix.html: add documentation on compilation on 64-bit systems
28-07-2008 J-Donald Tournier <d.tournier@brain.org.au>
* cmd/dwi2tensor.cpp: fix option parsing to allow multiple ignoreslices and ignorestudies instances
24-07-2008 J-Donald Tournier <d.tournier@brain.org.au>
* src/mrview/sidebar/orientation_plot.cpp: added support for overlay of orientation plot on main window
22-07-2008 J-Donald Tournier <d.tournier@brain.org.au>
* lib/mrtrix.h: fix va_list handing in printf()
21-07-2008 J-Donald Tournier <d.tournier@brain.org.au>
* lib/data_type.cpp: add definitions for all static const declarations
to avoid linking errors.
21-07-2008 J-Donald Tournier <d.tournier@brain.org.au>
* sysconf/linux.py: add '-fPIC' flag to compiler command
18-07-2008 J-Donald Tournier <d.tournier@brain.org.au>
* build: handle 'command not found' cases and provide a more helpful error message
15-07-2008 J-Donald Tournier <d.tournier@brain.org.au>
* improve support for 64 bit systems (thanks to Sebastian Jentschke for helping out):
- remove use of MR::Offset
- use gsize for most file operations
- use gssize where a signed quantity is required
14-07-2008 J-Donald Tournier <d.tournier@brain.org.au>
* src/mrview/sidebar/tractography/track_list_item.h: fixed Track::index() for use on 64 systems.
now uses gsize rather than guint in pointer arithmetic
11-07-2008 J-Donald Tournier <d.tournier@brain.org.au>
* lib/image/format/mri/cpp: fixed TMPFILE_ROOT_LEN - now set to 7
09-07-2008 J-Donald Tournier <d.tournier@brain.org.au>
* src/mrview/sidebar/orientation_plot.cpp: set color using config file
* Doxyfile: version number upped to 0.2.4
* lib/mrtrix.h: MRTRIX_MICRO_VERSION upped to 4
=======================================================================
VERSION 0.2.3
=======================================================================
09-07-2008 J-Donald Tournier <d.tournier@brain.org.au>
* lib/mrtrix.h: added getline() method to handle Unix/DOS end-of-line
* cmd/import_tracks.cpp: new command to import tracks stored
in ascii text files into MRtrix format for display in MRView
08-07-2008 J-Donald Tournier <d.tournier@brain.org.au>
* doc: amend documentation to describe configuration files
* src/mrview/sidebar/orientation_plot.cpp: add option to disable tri-linear interpolation
* src/mrview/sidebar/main.cpp: rename "diffusion profile" to "orientation plot"
also renamed src/mrview/sidebar/diffusion_profile.* accordingly
* lib/image/format/analyse.cpp: issue info statement about left-right encoding
* lib/file/config.h: fixed get_int() & get_float()
They were previously declared as returning bool
* lib/file/config.cpp: fixed get_int() & get_float()
They were previously defined as returning bool
* cmd/csdeconv.cpp: use NumberOfThreads entry in config file
rather than NUMBER_OF_PROCESSORS environment variable
07-07-2008 J-Donald Tournier <d.tournier@brain.org.au>
* cmd/disp_profile.cpp: remove use of Math::Matrix::transpose()
to flip row vector (transpose expects square matrices)
* cmd/csdeconv.cpp: fix multithreading
- map SH_obj before launching threads
- set/test against boolean "done" for end of data
04-07-2008 J-Donald Tournier <d.tournier@brain.org.au>
* src/quaternion.h: test for rounding errors in Quaternion::from_matrix().
In certain cases, a negative number was passed to sqrt()
* Doxyfile: version number upped to 0.2.3
* lib/mrtrix.h: MRTRIX_MICRO_VERSION upped to 3
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