changelog

Date	Software	Version	Description
2016.02.29	ROIEditor	1.8	* This version is compatible with Win8 and Win10. * The multilevel analysis function is updated.
2014.04.29	DiffeoMap	1.9	* The two models "2D affine" and "2D rigid" are added to the AIR Linear function. * The bias correction function is added to DiffeoMap. * The operation function is added to DiffeoMap. * The intensity scaling option is added to the opening image function. * The JHU_MNI_SS_BPM_TypeI_V2.1 atlas images and the JHU_MNI_SS_BPM_TypeII_V2.1 atlas images are added to DiffeoMap.
2014.04.29	ROIEditor	1.7	* A new roi object can be inserted in the roi object list. * The skull strip function is updated. * The JHU_MNI_SS_DP tracts created by Muwei Li are added to ROIEditor. * The multilevel analysis function is added to ROIEditor. * The intensity scaling option is added to the opening image function. * The quantitative analysis function is added to ROIEditor. * The "Generate Color Image" function can generate gray scale level color maps and green/red color maps. The scaling option is added to this function. * The option "Raw Data and Label Lookup Table" is added to the Load ROI function.
2013.02.01	DiffeoMap	1.8	* Mutual information slice by slice registration is available. * A bug is fixed in landmark-based reorientation on tensor. * A bug is fixed in remote lddmm. * In the "Manual Histogram Matching" function, the range of the scale is changed to 0.25-4.00. * JHU_MNI_SS_WMPM_TypeI is renamed as JHU_MNI_SS_BPM_TypeI_originl. JHU_MNI_SS_WMPM_TypeII is renamed as JHU_MNI_SS_BPM_TypeII_original. JHU_MNI_SS_WMPM_TypeIII is renamed as JHU_MNI_SS_BPM_TypeIII_orginal. JHU_MNI_SS_BPM_TypeII_V2.0 is added. * JHU_MNI_SS_GreMag_ss and JHU_MNI_SS_QSM_ss are added. * JHU_MNI_SS_EvePM_V1.0 and JHU_MNI_SS_EveDGMPM_V1.0 are added.
2013.02.01	ROIEditor	1.6	* The "skull stripping" function is updated. The default parameter values are changed. * The kernel size of the "Smooth ROIs" function can be set. * The new "Delete All" function can delete all ROI objects all at once. * The lable lookup tables are updated. * A analyze ROI file can be loaded into ROIEditor as ROI in analyze format even there is no roieditor-defined header file. * JHU_MNI_SS_WMPM_TypeI is renamed as JHU_MNI_SS_BPM_TypeI_originl. JHU_MNI_SS_WMPM_TypeII is renamed as JHU_MNI_SS_BPM_TypeII_original. JHU_MNI_SS_WMPM_TypeIII is renamed as JHU_MNI_SS_BPM_TypeIII_orginal. JHU_MNI_SS_BPM_TypeII_V2.0 is added. * JHU_MNI_SS_GreMag_ss and JHU_MNI_SS_QSM_ss are added. * JHU_MNI_SS_EvePM_V1.0 and JHU_MNI_SS_EveDGMPM_V1.0 are added.
2012.02.01	ROIEditor	1.5	* Make the boundaries of ROIs smoother. * Include the new JHU_MNI_SS tracts.
2011.10.24	ROIEditor	1.4.4	* A bug is fixed. This bug happened when a drawn ROI on a non-isotropic image was added to a ROI object.
2010.12.21	ROIEditor	1.4.3	* Generate color images based on different colormaps. * Generate ROI-based float images based on lookup tables. * Generate a mask on active image or each image in statistics calculation. * Generate a mask on active image or each image in tract specific probabilistic quantification. * Exclude image pixels or tract probabilities in tract specific probabilistic quantification. * Save current slice or all slices in bmp format. * Generate a more symmetric ROI when an ellipse is added to a ROI object. * Change the format of ROI statistics profile report. * Change the default values for the skull stripping function.
2010.12.21	DiffeoMap	1.7.2	* Add nine parameter model to AIR alignlinear registration. * Slice by slice AIR alignlinear registration. * Allow two matrices to be combined even if the template in the last transformation is not isotropic and give the warning message "Do not transform tensor data using this combined matrix.".
2010.09.16	DtiStudio	3.0.3	1. A new method for tensor calculation, Image Registration between theory and original DWI pairs, are implemented in this version. With this method, the original DWI will be co- registered with its theoretical one (which is derived from the estimated tensor and diffusion gradient) iteratively during tensor calculation process. Two methods, AIR and Mutual Information Registration, are available for image registration within this new method. 2. it now supports Philips Enhanced DICOM format, both in "MriView 3D" and "DTI Mapping" functions. 3. For Philips Enhanced DICOM files, the program can retrieve the gradients directly from their file header.
2010.08.02	DiffeoMap	1.7.1	A bug was fixed in the multi-channel remote lddmm function.
2010.07.30	DiffeoMap	1.7	* Mutual Information Registration is available. * AIR linear registration also works on 2D images. * Users can get the inverse of the landmark-based affine, rigid, or translation matrix. * Landmark file format is changed to display information on one line, eg. ID x y z. * Users can get a half lddmm map.
2010.06.18	ROIEditor	1.4.2	More digits are displayed when a pixel value is smaller than 0.01.
2010.03.23	DtiStudio	3.0.2	1. A new pixel-based outlier rejection method for tensor calculation. With this method, only the outlier pixels, not the outlier image slices, will be discarded during iterative tensor calculation. This method also takes account of the negative effects caused by mis-alignment between the image slices. By this new approach, the original image data points can be used as many as possible, and the signal to noise ratio of the results can be significantly improved. 2. it now supports Philips 4-dimensional DICOM format. 3. it now supports multiple-repetition Siemens Mosaic format. 4. for users convenient, some mostly used gradient tables are pre-defined as a user-selectable drop-down list within this updated program, 5. for Siemens Mosaic files, the program can retrieve the gradients directly from the file header.
2009.09.18	DiffeoMap	1.6	* Landmarker was renamed to DiffeoMap to represent its function more accurately. * After the transformations, the updated images can be automatically saved. * The buttons for all landmark-based transformations are moved to the tool panel.
2009.09.09	DtiStudio	3.0.1beta	1. DtiStudio can read NifTi single file format with "MRI View 3D" command now.Users don't need to convert NifTi into Analyze dual-files any more. 2. This updated version can read Big-Endian DICOM files. if the dataset is saved by a non-Intel machine (e.g. Motorola 68xxx), it may have a good chance that the DICOM files is in Big-Endian format. with this version, DtiStudio can rebuild this kind of images correctly. 3. Fiber file information displaying. When you try to load a pre-saved fiber data file (which was saved as default format) into current working-space using "File->Load Fiber Data" command, the fibers may not been able to overlaid onto the images correctly if the parameter of the fiber doesn't match with that of image. A pop-up message window will show the fiber parameters in such cases, to help uers locating the errors. 4. DtiStudio can save "Fiber Density Map" as a new kind of fiber tracking results. In this image map, each pixel contains the number of fibers passing through the pixels. So you can get a general idea about "fiber density" after fiber tracking from this image map. the density map can also be normalized into (0..1) by the biggest number of the fibers of all pixels. this function is available by clicking "Fiber-Save" button in the "Fiber" tab. 5. New method of tensor calculation. Pervious pixel-based automatic outlier rejection algorithm has been improved (thanks for Yue Li's significant contributions). The new algorithm uses weighted least-square regression model combined with error-points clustering approach, try to eliminate the bad pixels and minimize the square-errors by weighting the original signals based on the error-map between original and theoretical ones.
2009.05.29	ROIEditor	1.4.1	A bug was fixed. The feature "Exclude some pixels by setting the range of their intensities" now also works in the functions "Statistics for One ROI Object", "ROI Axial Profile", "ROI Sagittal Profile", "ROI Coronal Profile" and "Export Pixel Value".
2009.05.20	Landmarker	1.5.1	A bug was fixed in the "Save Transformation Matrix" function.
2008.05.14	Landmarker	1.5	* The atlas sample images are updated. New WMPM data for ICBM_DTI_81 and JHU_MNI_SS are added. * Users can do multiple alpha volume lddmm transformation. * A potential numerical error related to tensor data transformation has been fixed. Now the software can correctly handle tensor data with values less than 10^(-6). * Users can copy the current displayed image slice. * The process of landmark-based lddmm transformation is upgraded and can run faster. * When the image data format is changed to byte or word, there are three options: Automatic Scaling, Manual Scaling and No Scaling. * NIFTI images can be loaded to the software.
2009.05.14	ROIEditor	1.4	* The atlas sample images are updated. New WMPM data for ICBM_DTI_81 and JHU_MNI_SS are added. * Users can exclude some pixels in statistical calculation of all ROI objects in all images by setting the range of their intensities. * Users can copy the current displayed image slice. * Statistical data are displayed in four decimal points. * Users can grow or shrink a ROI object. * Users can export the vector values of the pixels contained in a ROI object. * NIFTI images can be loaded to the software.
2008.10.13	Landmarker	1.4	A bug was found in the tensor / vector reorientation algorithm of all the previous Landmarker versions, Version 1.0.1, Version 1.1, Version 1.1.1, Version 1.2 and Version 1.3. * A bug affects the linear and non-linear registration of tensor data (.d). When the transformation involves shearing operations, the tensor orientation was not properly re-oriented. * This affects tractgraphy after registration. * This does not affect scalar values such as FA, ADC, and eigenvalues. * We strongly encourage you to download Version 1.4 and reprocess your registered images. For the reprocessing, you simply need to reapply the stored transformation matrices using the new version (Version 1.4) because transformation matrices are not affected by the bug.
2008.09.09	DtiStudio	3.0.0beta	* More Details * Automatic outlier rejection for tensor calculation. * Verify the tensor calculation result by creating DWI-Fitting and DWI-Error maps. * Save the tensor calculation results just by few clicking * More optional results after tensor calculation * Three dimensional seeded regional growing function * Fiber statistics output format is updated.
2008.08.01	Landmarker	1.3	* ROI-based Manual Intensity Matching * Resample all loaded images at one time * Manual scaling when the data format of an image is changed to byte * Invert AIR Linear Matrix * Jacobian calculation of a LDDMM map * Disable tensor reorientation
2008.08.01	ROIEditor	1.3	* The data format of the ROI data file created by ROIEditor is changed to WORD. * Hide all ROIs and show all ROIs * Calculate the RGB of color images. * Double click a ROI and the corresponding ROI object box in the ROI object list will be highlighted. * Users can decide if zero is treated as no data in statistical calculation.
2008.04.24	Landmarker	1.2	* Modify atlas data * Crop vtk format LDDMM map * Automatic histogram matching
2008.04.24	ROIEditor	1.2	* Modify atlas data * Load Tensor * Fix all ROIs and unfix all ROIs * Change ROI header file * Skull strip(beta version) * Export pixel values * T2 calculation
2008.01.03	Landmarker	1.1.1	Fixed the image file ICBM_MNI_WMPM
2007.12.21	ROIEditor	1.1.1	Fixed a bug in the ICBM-MNI automated white matter parcellation report
2007.10.12	Landmarker	1.1	* Landmark-based lddmm * Multichannel volume lddmm * Intensity correction * Load a command file to modify an image * New sample images
2007.09.28	DTI Studio	2.4.1	* Registration * gradient adjustment * Additional I/O Formats
2007.09.12	ROIEditor	1.1	* Arithmetic operations * Add one more atlas ICBM-MNI * New sample images

ChangeLog LDDMM Service

# ChangeLog:
#
# 2013.02.08 - aek - Path to zip using LDDMM_VMM_DIR instead of HOME
#
# 2013.02.05 - aek - 2.0.8 - Copied 2.0.5 and added $ZIP feature.
#                    ** 2.0.6 and 2.0.7 had a bug with more than 9 channels
#                    ** MORE THAN 9 CHANNELS IS NOT WORKING **
#                    ** using $ZIP for zipping files to support zip64.
#
# *2013.01.31 - aek - 2.0.7 - using $ZIP for zipping files to support zip64.
#
# *2012.12.21 - aek - 2.0.6 - fixed bug to allow more than 9 channels.
#                    ATLAS_LIST and TEMPLATE_LIST generation correction.
#
#
# 2011.04.26 - aek - 2.0.5 "$COMMAND_NAME" = "lddmm-volume" needs KEEP_DIR
#                    and LDDMM_VMM defined.
#
# 2011.04.19 - aek - 2.0.4. Force directory creation. -K uses mmlddmm_ver4.0.2-verbose
#
# 2011.01.08 - aek - ** updated VTK_combine_maps to VTK_combine_maps_ver5_io11
#
# 2011.01.07 - aek - ** reverted VTK_combine_maps to VTK_combine_maps.old
#
# 2010.12.28 - aek - lddmm 2.0.3 now using mmlddmm_ver4.0.0
#
# 2010.12.10 - can - implemented new histogram matching.
#
# 2010.09.28 - aek - If command line is lddmm-volume or -S, single channel
#
# 2010.09.15 - aek - lddmm 2.0.1 now using mmlddmm_ver3.4.2
#
# 2010.09.08 - aek - Added -K option. This conforms to lddmm-volume output
#
# 2010.08.30 - aek - lddmm 2.0.0 now using mmlddmm_ver3.4.1.
#
# 2010.08.30 - aek - added finalMetricDistance.txt to Result.zip.
#
# 2009.06.09 - aek - Corrected error in -c option not being in current
#                    directory. 'LAST_WORD' and 'FULL_PATH' are used.
#
# 2009.05.19 - aek - Corrected error in copying multiple config files to the
#                    result directory. 'TMP_CONFIG_NAME' used to correct
#                    the problem.
#
# 2009.03.13 - aek - If '-c' is used the config  name is copied to
#                    the output. (lddmm-vmm.conf or lddmm.conf ...)
#
# 2009.03.13 - aek - Corrected 'if' test.
#                         if [-f "$TMP_INPUT/identity.txt" ]; then
#
# 2009.03.06 - aek - If 'identity.txt' doesn't exist, don't copy nonexistant
#                       files.
#
# 2009.02.05 - aek - Kimap.vtk and Hmap.vtk are produced for all variations
#                    of lddmm processing.
#
# 2009.01.27 - aek - Combine the mapping files using VTK_combine_maps.
#
# 2009.01.02 - aek - Implement Kenichi's method. (Ignore RESTART value)
#                       Note:  RESTART will be used after Xin udates
#                              her software
# 2008.10.30 - aek - Implemented Alpha option and memory estimation test.
#