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eg. Qdec = fReadQdec('qdec.table.dat');
    Qdec = rmQdecCol(Qdec,1);
    sids = Qdec(:,1);
eg. Qdec = fReadQdec('qdec.table.dat'); 
    Qdec = rmQdecCol(Qdec,1); 
    sids = Qdec(:,1); 

Longitudinal Statistics

LME Matlab tools. Author: Jorge Luis Bernal Rusiel, 2012. jbernal@nmr.mgh.harvard.edu or jbernal0019@yahoo.es

If you use these tools in your analysis please cite:

Bernal-Rusiel J.L., Greve D.N., Reuter M., Fischl B., Sabuncu M.R., 2012. Statistical Analysis of Longitudinal Neuroimage Data with Linear Mixed Effects Models, NeuroImage, doi:10.1016/j.neuroimage.2012.10.065.

These Matlab tools are freely distributed and intended to help neuroimaging researchers when analysing longitudinal neuroimaging (LNI) data. The statistical analysis of such type of data is arguable more challenging than the cross-sectional or time series data traditionally encountered in the neuroimaging field. This is because the timing associated with the measurement occasions and the underlying biological process under study are not usually under full experimental control.

There are two aspects of longitudinal data that require correct modeling: The mean response over time and the covariance among repeated measures on the same individual. I hope these tools can serve for such modeling purpose as they provide functionality for exploratory data visualization, model specification, model selection, parameter estimation, inference and power analysis including sample size estimation. They are specially targeted to be used with Freesurfer's data but can be used with any other data as long as they are loaded into Matlab and put into the appropriate format. Here are some recommendations about how to use these tools.

Preparing your data

There are two types of analyses that can be done: univariate and mass-univariate. The first step is to load your data into Matlab. If you are working with Freesurfer then univariate data (eg. Hippocampus volume) can be loaded using Qdec tables. There are, under the Qdec directory, some simple example scripts for reading and writing Freesurfer's Qdec tables.

In order to read mass-univariate data you should use the following scripts:

fs_read_label.m fs_read_surf.m fs_read_Y.m

The last two depend on Freesurfer's scripts so you need to have installed Freesurfer software package and included the Freesurfer's matlab subdirectory in the Matlab's search path.

Previously, the mass-univariate data is generated in Freesurfer by running variants of the following commands:

mris_preproc --qdec qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh (assembles your thickness data into a single lh.thickness.mgh file)

mri_surf2surf --hemi lh --s study_average --sval lh.thickness.mgh --tval lh.thickness_sm10.mgh --fwhm-trg 10 --cortex --noreshape (smooths the cortical thickness maps with FWHM=10 mm. Note the --cortex and --noreshape options)

Then you can load the cortical thickness data lh.thickness_sm10.mgh into Matlab using

fs_read_Y.m eg. [Y,mri] = fs_read_Y('lh.thickness_sm10.mgh');

You should also read the spherical surface (lh.sphere) and cortex label (lh.cortex.label) of study_average.

eg. lhsphere = fs_read_surf('$FsDir/freesurfer/subjects/fsaverage/surf/lh.sphere');

  • lhcortex = fs_read_label('$FsDir/freesurfer/subjects/fsaverage/label/lh.cortex.label');

Once you have your data in Matlab you need to build your design matrix. For computational efficiency reasons, these tools require the data ordered according to time for each individual (that is, your design matrix needs to have all the repeated assessments for the first subject, then all for the second and so on). You can use the script:

sortData

For example, if you have your covariates in a Qdec table then you can use the following code

eg. Qdec = fReadQdec('qdec.table.dat');

  • Qdec = rmQdecCol(Qdec,1); sids = Qdec(:,1); Qdec = rmQdecCol(Qdec,1); M = Qdec2num(Qdec); [M,Y,ni] = sortData(M,2,Y,sids);

Model specification

Parameter estimation

Model selection

Inference

Power analysis

Example data analyses

LongitudinalStatistics (last edited 2018-07-25 12:06:32 by MorganFogarty)