SpmFlirt - MRC CBU Imaging Wiki

Upload page content

You can upload content for the page named below. If you change the page name, you can also upload content for another page. If the page name is empty, we derive the page name from the file name.

File to load page content from
Page name
Comment
In thi sntence, what word is mad fro the mising letters?

Revision 2 as of 2013-03-07 21:22:57

location: SpmFlirt

Using FLIRT to coregister EPI and structural

The software is installed at the CBU. For those outside the CBU, you will need the Oxford software bundle which includes a variety of versions of the Brain Extraction Tool (BET), and the image registration program FLIRT. These programs need to be on your executable path. You also need some matlab m files I wrote (bet.m flirt.m flirt_coreg.m), available via this Flirt http directory. These m files need to go on your matlab path.First, create a version of the structural image with the skull and scalp removed, using BET. Start SPM, and from the matlab prompt (>>), type

bet

Select the structural image(s) to skull strip and let the program run. You now have skull stripped versions of the structural images prefixed with 'ss_'.To run the EPI -> structural coreg, go the the >> prompt in the matlab window, and type:

flirt_coreg

Select number of subjects, coregister only, then select the skull stripped structural image as the target, the mean EPI image as the object image, and as 'Other images', select the EPI time series (slice time corrected, after realignment) (a000*img usually). Choose Correlation ratio as the cost function, and 'RB zooms and shears (12)' for the 'Degrees of freedom'. Check the eventual output; thence you can normalize the structural and reslice the EPI images etc.You might consider using linear only normalization, or normalization with few nonlinear basis functions; the remaining imperfect match between the EPI and structural image means that the higher detail warps calculated for the structural may be applied to the wrong area of the functional.

Matthew Brett 26/10/00