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SVReg : Changelog

Version 21a

  • USCBrain atlas is now included with the release
  • Workflow is changed. svreg -> corticalthickness estimation -> map to atlas -> statistics computation

  • Separate executables for surface and volume registration, cortical thickness estimation, mapping thickness to atlas, and statistical computation.

  • Separate executables for running a combined workflow that contains surface and volume registration, cortical thickness estimation, mapping thickness to atlas, and statistical computation.

Version 18a

  • Executable for resampling the volumes is added
  • Executable for changing the atlas
  • Several bug fixes

Version 17a

  • Executable for volumetric smoothing
  • MNI to Talairach coordinate conversion. A new script is included in the release that will do this coordinate conversion.
  • A new executable that compute ROIwise stats for any parameters (e.g. FA, MD maps) is included.
  • Several bug fixes

Version 16a

  • A new flag (-U) added for single threaded mode
  • Executable for manual bias field correction is added to the distribution
  • Executable for application of SVReg forward or inverse map to scalar or tensor images is added to the distribution

Version 15b

  • Negative Jacobians are significantly reduced in this version

Version 15a

  • Inverse map is now saved in the main subject directory by default. Forward map was always saved.
  • The cortical labels are constrained by intersection of pial surface mask and cerebrum mask. i.e. the dilated surface mask is constrained to the cerebrum mask.
  • PVC fraction map of subject mapped to atlas and atlas mapped to subject are saved in the temp directory.
  • Jacobian of the deformation field is now saved in the temp directory.
  • Better cerebellum alignment is performed by initializating the cerebellum alignment using AIR based deformation field.
  • Hippo-carved mask is edited in the BrainSuiteAtlas1 and BCI-DNI_brain atlas.
  • Several atlas files for BCI-DNI_brain atlas are updated, including bfc and label files that address minor issues in brain mask and labels.
  • ROI 740 is used as an exception that can lie inside or outside the pial surface/cerebrum mask.
  • This version tries to create an invertible deformation field by iteratively inverting the deformation field. Iterative map correction is used. –S flag can be used to perform this correction selectively to areas with non-positive Jacobians.
  • Thickness computation script is now added to SVReg distribution.
  • AIR registration is used instead of the affine registration field. This improves the accuracy of the cerebellum coregistration.
  • By default, accurate alignment of white matter mask (dewisp mask) is emphasized at the cost of non-diffeomorphic mapping at the sulcal banks. However, if user wants to emphasize diffeomorphism, then we recommend Regularization of 5 by specifying ‘-S 5‘ in the command line. This performs a decent job of aligning the cortex, though it is not exact, and also gives good Jacobian performance and invertibility.
  • There were issues about alignment of cerebellum in the previous version. This issue is fixed by initializing deformation field outside cerebrum mask by AIR deformation field.
  • Gray matter sometimes got labeled as a gyral white in SVReg14c. Does not seem to happen now due to improved cortical alignment.
  • Header of the svreg.nii.gz file is fixed now which should show better alignment.
  • A new flag -P allows multithreaded execution on the command line.
  • Several minor bug fixes are incorporated into this version.

Version 14c

  • Extension of deformation field from white matter to the rest of the brain is performed using Laplacian based regularizer instead of the linear interpolation.
  • This version uses partial fraction tissue classification image (pvc.frac) instead of the bias field corrected T1 image (.bfc) for the purpose of intensity registration.
  • Intensity registration is performed using native matlab code and preconditioned conjugate gradient method instead of the external compiled matlabcentral code that used lbfgs optimization.
  • Hippocampus and Amygdala are coregistered using intensity information rather than surface constraints.
  • Cerebellum is coregistered using intensity registration by modifying the deformation field generated from previous steps.
  • One single deformation field is computed with better Jacobian performance.
  • The labels are constrained by a mask generated using the pial surface. A flag is added that can limit the size of the mask dilation or erosion.
  • Alternate to the pial surface mask, the cerebrum mask can also be used to limit the boundaries of the labels. There is a flag added which activates this functionality.
  • This version has more cross-compatibility in terms of results across platforms (Win,Mac,Linux).
  • Several minor bug fixes
  • Outputs one single svreg volume label file instead of multiple label files.

Version 14a

  • All intermediate files are stored in a temporary folder created in each subject directory.
  • svreg_prepare_files module is now removed, its functionality is incorporated into svreg_label_surf_hemi file.
  • Support for Oblique headers (xform,qform) in nifti headers is added.
  • -r flag is removed in Windows, Linux and Mac scripts. It is called by default in these script now.
  •  Global variables were removed. They were creating randomness in the outputs.
  • Several changes in registration process are made to make the outputs bit-compatible in mac and Linux. They are almost same, the differences are on the order of level of precision of the machines.
  • The new label scheme (dws volumetric labels) is incorporated into brain suite.
  • The new atlas (BCI-DNI_atlas) is incorporated.
  • A log file is added that shows version number and the commands that are getting executed.
  • new labels for gyral WM added.
  • improved corsscompatibility
  • added cerebellum labeling code
  • bug fixes
  • -cbm flag for manual cerebrum mask
  • increased tolerance for load_nii to dont care about oblique header
  • updated the ‘unknown’ label in the surfaces.
  • Also corrected the volume labels.
  • fixed WM label to be = 3 instead of 2
  • updated the files such that if there is a space in the path, then the code still works.

Version 0.94

  • Map2atlas_thickness module is deleted.
  • label2.nii renamed to ref.label.nii.gz
  • label2.nii renamed to ref.label.nii.gz
  • label3.nii renamed to svreg.wm.label.nii.gz
  • label4.nii renamed to svreg.corr.label.nii.gz
  • reg extensions changed to svreg