- Notifications
You must be signed in to change notification settings - Fork20
MATLAB code for reading and writing CIFTI connectivity files
License
Washington-University/cifti-matlab
Folders and files
| Name | Name | Last commit message | Last commit date | |
|---|---|---|---|---|
Repository files navigation
This library is compatible with the CIFTI-2 format, withoutexternally installed dependencies (except that CIFTI-1 files requirewb_command for conversion), returning a structure that exposes theinformation contained in the CIFTI-2 XML with minimal translation, as wellas the data matrix with no added padding. The cifti_read function isthe intended starting point, ciftiopen and similar are compatibilitywrappers so that the library can be used in older code.
Additionally, the library provides numerous helper functions to make manycommon operations (such as extracting the data for one structure) into asingle line of intuitive code.
The previous code that was derived from FieldTrip is in the "ft_cifti"folder.
The cifti structure returned by this library uses 0-basedindices for vertex and voxel indices, 1-based for cifti indices, andthe helper functions return 1-based indices for everything.
All exposed functions have usage information available through thehelp command:
>> help cifti_read function outstruct = cifti_read(filename, ...) Read a cifti file....The simplest practical usage is to load a cifti file withcifti_read, takeits data from the.cdata field, modify it, store it back into the.cdata field,and write it back out to a new file withcifti_write:
mycifti= cifti_read('something.dscalar.nii');mycifti.cdata= sqrt(mycifti.cdata);cifti_write(mycifti,'sqrt.dscalar.nii');
Theciftiopen,ciftisave, andciftisavereset functions provide backwardcompatibility with a previous cifti library (option II ofHCP FAQ 2),and you can also use thisciftisavereset function even if you usecifti_read.An alternative way to do the equivalent ofciftisavereset is to use thecifti_write_from_template helper function (which also has options to setthe names of the maps for dscalar, and similar for other cifti file types):
mycifti= cifti_read('something.dscalar.nii');cifti_write_from_template(mycifti,mycifti.cdata(:,1),'firstmap.dscalar.nii','namelist', {'map #1'});%ciftisavereset equivalent (keeping 'mycifti' unmodified):mycifti= cifti_read('something.dscalar.nii');newcifti=mycifti;newcifti.cdata=mycifti.cdata(:,1);ciftisavereset(newcifti,'firstmap.dscalar.nii');clearnewcifti;
Thecifti_struct_create_from_template function can create a cifti struct without writingit to a file, with the same options ascifti_write_from_template to control the otherdiminfo. Thecifti_write... orcifti_struct... functions should handle most cases ofworking with common cifti files, including extracting the data for one cortical surface,doing some computation on it, and replacing the surface data with the new values:
mycifti= cifti_read('something.dscalar.nii');leftdata= cifti_struct_dense_extract_surface_data(mycifti,'CORTEX_LEFT');newleftdata=1-leftdata;newcifti= cifti_struct_dense_replace_surface_data(mycifti,newleftdata,'CORTEX_LEFT');...
Thedense part of some function names refers to only being applicable to "dense" filesor diminfo (in cifti xml terms, a "brain models" mapping), such as dtseries, dscalar,dlabel, or dconn. There are moredense helpers mainly because there is a more commonneed to make use of the information in a dense diminfo than most other diminfo types.
Thecifti_diminfo_* helpers are lower-level and require more understanding of thedetails of the cifti format, and often require writing more code to use them, so youshould generally look at thecifti_write... andcifti_struct... functions first.
outstruct = cifti_read(filename, ...)cifti_write(cifti, filename, ...)cifti = ciftiopen(filename, ...) %note: these 3 do not use option pairs,ciftisave(cifti, filename, ...) % the varargin here is to make passing 'wb_command' optionalciftisavereset(cifti, filename, ...)cifti = cifti_struct_create_from_template(ciftitemplate, data, type, ...)cifti_write_from_template(ciftitemplate, data, filename, ...)cifti = cifti_struct_create_sdseries(data, ...)cifti_write_sdseries(data, filename, ...)[outdata, outroi] = cifti_struct_dense_extract_surface_data(cifti, structure[, dimension])cifti = cifti_struct_dense_replace_surface_data(cifti, data, structure[, dimension])[outdata, outsform1, outroi] = cifti_struct_dense_extract_volume_all_data(cifti[, cropped, dimension])cifti = cifti_struct_dense_replace_volume_all_data(cifti, data[, cropped, dimension])[outdata, outsform1, outroi] = cifti_struct_dense_extract_volume_structure_data(cifti, structure[, cropped, dimension])cifti = cifti_struct_dense_replace_volume_structure_data(cifti, data, structure[, cropped, dimension])[surflist, vollist] = cifti_diminfo_dense_get_structures(diminfo) %returns the names of structures that exist in this diminfooutstring = cifti_metadata_get(metadata, key) %returns empty string for nonexistent keymetadata = cifti_metadata_remove(metadata, key) %returns unmodified metadata struct for nonexistent keymetadata = cifti_metadata_set(metadata, key, value) %overwrites key if it existsoutinfo = cifti_diminfo_dense_get_surface_info(diminfo, structure)outinfo = cifti_diminfo_dense_get_volume_all_info(diminfo[, cropped])outinfo = cifti_diminfo_dense_get_volume_structure_info(diminfo, structure[, cropped])outmap = cifti_diminfo_make_scalars(nummaps[, namelist, metadatalist])outmap = cifti_diminfo_make_series(nummaps[, start, step, unit])indices = cifti_vox2ind(dims, voxlist1) %helper to act like sub2ind for voxel ijk listsAbout
MATLAB code for reading and writing CIFTI connectivity files
Topics
Resources
License
Uh oh!
There was an error while loading.Please reload this page.
Stars
Watchers
Forks
Uh oh!
There was an error while loading.Please reload this page.
Contributors3
Uh oh!
There was an error while loading.Please reload this page.