Release Name: 0.2.7
Notes:
This release fixes a potentially problematic bug that caused incorrect scaling of the FA values. The FA values produced by previous versions of MRtrix were underestimated by approx. 22.5%. Any users that rely on MRtrix to produce FA values are urged to regenerate their FA maps using this new version.
Also included are some tools to ease integration with other spatial normalisation packages, as well as a command-line ROI statistics tool.
Changes:
=======================================================================
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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