calcFD toolbox

A toolbox for MATLAB for calculating the fractal dimensionality of a 3D structure, designed to work with intermediate files from FreeSurfer analysis pipeline, but can also use other volumes.

To use the toolbox with data in NIfTI format, see example_nii in examples.

Current public version: build 31 [20180517]

Citing the toolbox

Please cite this paper if you use the toolbox:

• Madan, C. R., & Kensinger, E. A. (2016). Cortical complexity as a measure of age-related brain atrophy. NeuroImage, 134, 617-629. doi:10.1016/j.neuroimage.2016.04.029

If you use the toolbox with subcortical/ventricular structures, please also cite:

• Madan, C. R., & Kensinger, E. A. (2017). Age-related differences in the structural complexity of subcortical and ventricular structures. Neurobiology of Aging, 50, 87-95. doi:10.1016/j.neurobiolaging.2016.10.023

Also see:

• Madan, C. R., & Kensinger, E. A. (2017). Test-retest reliability of brain morphology estimates. Brain Informatics, 4, 107-121. doi:10.1007/s40708-016-0060-4
  

Documentation

% Calculate the fractal dimensionality of a 3D structure. % Designed to work with intermediate files from FreeSurfer analysis pipeline % (ribbon.mgz, aparc.a2009s+aseg.mgz, and others). % Also can use other mgz volume as input (e.g., see 'benchmark folder'). % % See 'wrapper_sample.m' for an example of how to use the calcFD toolbox. % % REQUIRED INPUTS: % subjects = list of subjects names in a cell array % alternatively accepts {'.'} to run on all subjects in folder % % subjectpath = FreeSurfer 'SUBJECTDIR' where standard directory structure is % % options = specify details of running the analysis % % options.alg = 'dilate' | 'boxcount' % % options.countFilled = 0 | 1 % 0 == Surface-only (FDs) % 1 == Filled volume (FDf) % % options.aparc = 'Ribbon' | 'Dest_aparc' | 'Dest_select' | 'DKT' | 'Economo' | 'none' % 'Ribbon' == Cortical Ribbon (unparcellated) % 'Dest_aparc' == Parcellated cortical regions (Destrieux) % ** requires options.input. % 'Dest_select' == Any region in the aparc.a2009s+aseg.mgz volume, % ** requires options.input. % 'DKT' == Parcellated cortical regions (DKT). % ** requires aparc.DKTatlas+aseg.mgz (FS 6) or % aparc.DKTatlas40+aseg.mgz (FS 5.3) to exist. % The volume can be generated (FS 5.3) using: % mri_aparc2aseg --s [SUBJECTID] --annot aparc.DKTatlas40 % See Madan & Kensinger (2017, Brain Informatics) for further details. % 'Economo' == Parcellated cortical regions (von Economo-Koskinas). % ** requires economo+aseg.mgz to exist. % The volume can be generated using: % mris_ca_label, mris_anatomical_stats % See Scholtens et al. (2018, NeuroImage) and % Madan & Kensinger (2018, Eur J Neurosci) for further details. % 'none' == Binarized volume to be manually entered % (e.g., benchmark volumes). % % options.input = filename string, required for 'Dest_aparc' and 'Dest_select % if options.aparc == 'Dest_aparc' % This should be a file with the name 'mask_*.txt', % where * is the value in options.input. % File should have either 74 or 148 rows, only 1 column. % If only 74 values, labels are assigned bilaterally. % Value in each row is the label to assign to that parcellated region, % based on the Destrieux et al. (2010) parcellation scheme. % See 'mask_lobe.txt' for an example. % See 'calcFD_mask.xlsx' for a list of which regions correspond to each row number. % -- % if options.aparc == 'Dest_select' % This should be a file with the name 'select_*.txt', % where * is the value in options.input. % Regions correspond to intensity values in aparc.a2009s+aseg.mgz. % See FreeSurfer files (e.g., FreeSurferColorLUT.txt, ASegStatsLUT.txt, % WMParcStatsLUT.txt) for mapping of region intensities to names. % Multiple region values on the same row will be processed as a single structure. % Currently cannot use the same region in more than one row, % if need to violate this, use multiple input text files. % See 'select_subcort.txt' and 'select_ventricles.txt' for examples. % % options.output = filename string to output FD values to % % % OPTIONAL INPUTS: % options.boxsizes = list of numbers % Default: 2.^[0:4] (resolves to [1,2,4,8,16]) % Specify what 'box sizes' (also applies to dilation algorithm) to use % when calculating FD. % Preferred to scale in powers of two. % % ---- % % The calcFD toolbox is available from: http://cmadan.github.io/calcFD/. % % Please cite this paper if you use the toolbox: % Madan, C. R., & Kensinger, E. A. (2016). Cortical complexity as a measure of % age-related brain atrophy. NeuroImage, 134, 617-629. % doi:10.1016/j.neuroimage.2016.04.029 % % If you use the toolbox with subcortical/ventricular structures, please also cite: % Madan, C. R., & Kensinger, E. A. (2017). Age-related differences in the structural % complexity of subcortical and ventricular structures. Neurobiology of Aging, 50, 87-95. % doi:10.1016/j.neurobiolaging.2016.10.023 % % % 20180517 CRM % build 31