UJA-SHFD

2016-2020, Juan Ruiz de Miras and Guillermo Martínez Lledó. University of Jaén - SPAIN

UJA-SHFD is a MATLAB tool for computing the Spherical Harmonic Fractal Dimensions of surfaces. UJA-SHFD is especially designed for processing brain cortex surfaces obtained from the common pipeline of Freesurfer (pial and white surfaces). UJA-SHFD can also process surfaces in OBJ format.

UJA-SHFD has two operation modes: GUI and console. GUI mode allows the user to interactively compute the fractal dimensions of a surface: local fractal dimension, a map with a fractal dimension value for each vertex, and global fractal dimension, the fractal dimension of the entire surface. You can use the console mode to launch independent processes for processing several surfaces in batch or in parallel.

You can download the MATLAB source code of UJA-SHFD by clicking here

Two pre-processed examples can be downloaded here. You can use these two examples to rapidly test the application.


INSTALLATION

Only for Windows platform: Microsoft Visual Studio 2012 run-time libraries are required. You can download them directly from Microsoft web site at https://www.microsoft.com/en-US/download/details.aspx?id=30679


USAGE

At the MATLAB prompt:
>> uja_shfd : GUI
>> uja_shfd surface_file ['max_L' value] ['min_L_reg_local' value] ['max_L_reg_local' value]
['min_L_reg_global' value] ['max_L_reg_global' value] ['sigma' value]
['iterations' value]

As an independent process for batch or parallel processing of several surfaces:
matlab -nojvm -nodisplay -nosplash -nodesktop -r "uja_shfd surface ..."

EXAMPLES

>> uja_shfd "path_to_examples"/ujashfd_examples/lh.pial
Results will be stored in files lh.pial_localSHFD_1_900_21_40 and lh.pial_globalSHFD_11_29.txt.

>> uja_shfd "path_to_examples"/ujashfd_examples/lh_sim_10K.obj 'min_L_reg_local' 1 'max_L_reg_local' 20
Results will be stored in files lh_sim_10K.obj_localSHFD_1_900_1_20 and lh_sim_10K.obj_globalSHFD_11_29.txt.

CITATION

If UJA-SHFD has been useful for your research, please, cite as:
"A MATLAB tool for computing the spherical harmonic fractal dimension of the cerebral cortex"
Juan Ruiz de Miras, Guillermo Martínez-Lledó, William Orwig and Jorge Sepulcre
Computer Physics Communications, 2020 (https://doi.org/10.1016/j.cpc.2020.107381)


CONTACT AND SUGGESTIONS

For contact information click here