16.1

• move_to_submask and move_from_submask
• add support for writing older xiftis w/o "Other" level in sub labels
• fix subcortex bugs

15.1

v0.15.0

0.15.1 accepted to CRAN

14.0

Minor fixes and improvements.

13.0

13.2

ciftiTools now has a couple functions which make working with parcellations easier. (A parcellation is a single-column dlabel CIFTI or "xifti" object. Each label level, or "Key", represents a "parcel." Each location belongs to exactly one parcel. Parcels are usually contiguous regions--but not necessarily. ciftiTools includes a few of the most commonly-used parcellations. These can be loaded with load_parc. Any other parcellation CIFTI file can be read in with read_cifti.)

• apply_parc: Apply a parcellation "xifti" to a data "xifti". Can be used to compute the mean of each column, e.g. for FC calculation, but also supports applying any other function parcel-wise.
• parc_vals_to_xifti: Create a "xifti" from a parcellation and a numeric matrix of values corresponding to each parcel.

Other new functions:

• remap_cifti: an extension of resampling. Beware, we might revamp this function in the future.
• surf_area: computes the surface area attributable to each vertex or face of a "surf" object.

Changes to existing functions:

• convert_xifti, convert_to_dlabel: arguments related to levels & labels have been renamed to match factor more closely.
• separate_cifti and write_xifti2: now require users to provide either the write_dir argument, or file names for each desired output file. This gives users more flexibility to control which files are written.
• view_xifti qualitative color legend: add black outline.
• view_xifti, view_volume: print out indices of the selected subcortical slices.
• unmask_subcortex: now expects xifti input. If necessary, use the internal function ciftiTools:::unvec_vol to unmask a numeric matrix directly.

Bug fixes:

• view_xifti: fix bug where legend image was still written if legend_fname=NULL.

13.1 also includes misc. documentation and warning improvements.

12.0

New features

• Proper writing out of dlabel CIFTI data. Fixed problems if multiple columns or with subcortical data.
• Add even_vert_samp.
• Add apply_parc.
• Add set_names_xifti.
• Add NA_color argument to view_xifti_surface.
• Add shadows argument to view_xifti_surface.
• mask_surf takes in a "surf" object now.

Misc. documentation and warning improvements.

0.11.0

11.0 (Jan 23, 2023)

Changes to default behaviors

• Add crop to view_xifti_volume; the default is TRUE. Previously the subcortical images were cropped to the anatomical image; now the default is to crop them to the data.
• Change default of orientation_labels in view_xifti_volume to TRUE.
• Allow NA and NaN values in "xifti" objects with label data. Leave these values alone rather than making them into factor levels.
• Add warning if surface data are being upsampled
• Delete helper file surfaces written by smooth_cifti rather than returning their file paths.

New features

• Add adaptive resampling for surface data. The default remains barycentric.
• Add surface manipulation functions from BayesfMRI.
• Allow xii + mat (and other operations)
• Add scientific argument to view_xifti. By default, scientific notation is determined automatically (as before).
• Misc. patches

Documentation

• Add lit vs unlit comparison to README
• Improved citations

10.0 (July 5, 2022)

• Fix error during resampling when only one hemisphere is present
• Better file I/O on mounted Google Drive
• Add new viridis color palettes
• Coerce new data input to newdata_xifti to numeric
• Add file extension to file name in write_xifti automatically, if not provided

9.0

New features

• Add convention and orientation_labels to view_xifti_volume (default: neurological, instead of radiological as it's been previously)
• Add together_ncol to view_xifti_* to control compositing layout
• Add fname argument to view_comp to save the result to a PNG file
• Allow "xifti" objects to have different resolutions in the left and right cortex
• Add citation to welcome message

Behind-the-scenes improvements

• Better file path management for system commands
• Better use of S3 group methods for Math, Ops, Summary functions
• Replace coveralls with codecov
• Misc. patches

8.1

• Add more support for reading in v1 CIFTI files
• Better handling of file paths
• Better handling of optional "xifti" metadata
• remove_xifti can delete individual subcortical structures now
• Add scale_xifti which works like scale
• Fix resamp_res argument to make_surf (missing on CRAN 8.0)
• Update link to publication (missing on CRAN 8.0)

7.0

• Add view_comp, and the argument together to view_xifti_surface and view_xifti_volume
• Fixes to view_xifti_surface and view_xifti_volume
• Add limited support for v1 CIFTI
• Fix some file paths of written files
• Lower default surface smoothing from sigma = 5 to sigma = 3
• Add trans_units to subcortex metadata
• Rename write_cifti_components as write_xifti2 and export
• Add (in)equalities between "xifti" objects
• Add workbench download URL to start message.
• Add internal functions vox_locations and edit_mask_surf

6.1

• Revamped subcortical visualization with view_xifti_volume! Added tests for it.
• plot will now show both the cortex and subcortex, if both are present. The plots will share the color mode, color palette, and zlim.
• Revamped summary/print for "xifti" objects
• Faster border computation in read_xifti_surface