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mrInitRet is deprecated. The current function to initialize fMRI data is mrInit. We preserve this page as instructions for those who like to use very old code.

[edit] mrInitRet

mrInitRet is specialized for Lucas Center data: anatomical images in either DICOM or GE Genesis (I file) format, or functional images in a custom format (P*.7.mag) produced by Gary Glover's reconstruction code.

mrInitRet presents the user with a series of dialogs intended to be straightforward. The different preprocessing flags are described here. The following wizard will appear when you run mrInitRet.m


We normally select two or three options (shown). The crop option is OK, but not necessary.

When you crop the image, click upper left end of the image, and then click lower right end of the image.

FMRI reconstruction.jpg

Fill in the "Description", such as "retinotopy", and Subject. Also, you need to change "Initial frames to discard", and press "Copy" to copy the parameter to all sessions.

Data type editor.jpg

Fill in the "Description", such as "wedge" or "ring", and specify the "Number of cycles/scan". After you press "Accept", you'll chose the sessions you would like to analyze.

[edit] mrInitRetAnalyze

A variant of mrInitRet has been written to work with ANALYZE format files, mrInitRetAnalyze.m. (This routine is still missing a function, getScanParamsAnalyze, which should be checked in to the repository.)

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