November 10, 2021¶
Restructuring of intialisation script and a new stable docker image. See the installation page for the new form.
↪ split installation scripts into downloads and init | @caseypaquola
July 27, 2021¶
New option to define output resolution for volumes
↪ added optional "out_res" input parameter to bigbrainwarp | @caseypaquola
July 21, 2021¶
Overhauled naming conventions within BigBrainWarp, which led to changes in the input arguments for the main function. To reduce the size of the Docker image, Freesurfer functions have been purged and it is no longer a software dependency.
↪ implemented BIDS-style naming of files | @caseypaquola ↪ changed bigbrainwarp arguments, requires "desc" | @caseypaquola ↪ added option for 32k or 164k mesh for fs_LR | @caseypaquola ↪ removed Freesurfer dependencies | @caseypaquola ↪ created tutorial on evaluating transformations | @caseypaquola
April 7, 2021¶
Transformed staining intensity profiles to fs_LR and fsaverage (our first user request 🎂)
↪ added spaces/fs_LR/profiles_fs_LR.txt | @caseypaquola ↪ added spaces/fsaverage/profiles_fsaverage.txt | @caseypaquola
March 30, 2021¶
Added ICBM surface, allows transformations between bigbrain surface and icbm volume too. Created a wrapper script for generating staining intensity profiles
↪ added icbm surface template from civet | @caseypaquola ↪ added out_type option in bigbrainwarp | @caseypaquola ↪ created sample_intensity_profiles.sh | @caseypaquola
March 24, 2021¶
Transforming data with BigBrainWarp is greatly simplified. Users need only interact with the bigbrainwarp function.
↪ created bigbrainwarp base function | @caseypaquola ↪ expanded volume-based interpolation options | @caseypaquola
March 11, 2021¶
Cortical gradients are now available in volume space! We used registration fusion to project the gradient from fsaverage to icbm (Wu et al., 2018)
↪ Hist, Micro and Func gradients added to /spaces/icbm/ | @caseypaquola
March 4, 2021¶
Estimated layer thicknesses from Wagstyl et al., 2020 surfaces (ftp://bigbrain.loris.ca/BigBrainRelease.2015/Layer_Segmentation/3D_Surfaces/April2019/) and transformed to standard surface templates
↪ Pre-computed BigBrain layer thicknesses in /spaces/bigbrain/ | @caseypaquola ↪ Transformed layer thicknesses in fsaverage and /fs_LR | @caseypaquola
February 25, 2021¶
Changed all surface-based transformations to multi-modal surface matching, using new registrations from Lindsay Lewis. More details here.
↪ Overhaul of surface transformation scripts and documentation | @caseypaquola
February 8, 2021¶
Expanded the surface transformation functionality. Now supports (i) multi-modal surface registration via a parcel-based transformation and (ii) fs_LR for vertex-based nearest neighbour interpolation.
↪ Added approach option for surface based transformations | @caseypaquola ↪ Added surface option for fs_LR and fsaverage compatibility | @caseypaquola ↪ Updated documention for surface transformations | @caseypaquola