Minor fixes and improvements.


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 (Jul 28, 2023)

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.

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)

9.0 (May 16, 2022)

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

8.0 (February 1, 2022)

7.0 (November 16, 2021)

6.0 (September 13, 2021)

5.0 (August 31, 2021)

4.3 (August 14, 2021)

4.2 (August 10, 2021)

4.1 (August 7, 2021)

Changes affecting users

4.0 (August 4, 2021)

Changes affecting users

Notes for developers

3.1 (June 16, 2021)

Changes affecting users

Notes for developers

None # 3.0 (June 13, 2021)

Changes affecting users


2.2 (March 16, 2021)

Changes affecting users


Notes for developers

2.1 (March 15, 2021)

Changes affecting users

2.0 (February 2, 2021)

Changes affecting users

1.6.1 (January 29, 2021)

Changes affecting users

1.6 (November 10, 2020)

Changes affecting users

Notes for developers

1.5 (October 2, 2020)

Changes affecting users

1.4.2 (September 25, 2020)

Changes affecting users

Notes for developers

1.4 (August 31, 2020)

Changes Affecting Users

Demo files

Notes for Developers


It will be located here: https://htmlpreview.github.io/?https://github.com/mandymejia/ciftiTools/blob/master/vignettes/ciftiTools_vignette.html once we push to master. Until then, replace “master” with “1.4”

1.3 (August 24, 2020)

1.2 (August 7, 2020)

1.1 (July 24, 2020)

New names

Most of the functions were renamed. In general, cifti_[action] is now [action]_cifti. So to open and visualize a CIFTI file, one would use read_cifti() followed by view_cifti(). To save a resampled version of a CIFTI file, one would use resample_cifti().

Arguments were also renamed for consistency across functions:

New functionality

There are a few new functions:

And, a few new arguments:

Other updates:

Removed functionality

Notes for developers