SVReg Changelog

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 ==> svreg