This analysis package can implement the following steps in a streamline fashion: concatenating various runs, spatial filtering (smoothing), normalization, masking, hemodynamic response function modeling, and deconvolution/regression for TR-locked or irregular stimulus timing.

Go to the directory where you want to run the analysis of some dataset, start Matlab with "matlab -nodesktop" and type "IndiAna" at the prompt. You will be asked a list of streamlined and interactive questions, which would lead you to running some preprocessing steps and 3dDeconvolve with various options. It will generate output you usually would get from 3dDeconvolve. Moreover, it would also create a text file called *Log in which almost all command lines are saved. You can tweak some steps in the text file and rerun later at the shell prompt without resorting Matlab.

Once it reaches the point where 3dDeconvolve is implemented, a window would pop up showing the condition number for X'X (X is the experiment design). If that number is too big, for example in the order of 10^10, then it might indicate some problem with the design.

It is highly suggested that all the input command lines be saved in a text file for records or for rerunning the steps by simply copying and pasting.

No doubt the code is a little messy and there might be various bugs. Please kindly let me know when you encounter any problems running the script.

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