Normalizing fsl preprocessed image

Hi everyone,

I did subject-level preprocessing by fsl. So the preprocessed image is not normalized. I did “func → native → standard” registration and have all transformation files in the “reg” folder.
I don’t want to run a group-level analysis; how can I normalize the preprocessed image to standard space?


Hi @majidsaberi,

If you have all the transformation files, you should be able to just run flirt, supplying the transformation you have with -applyxfm (see the user guide here).

Although I do not know your goals with the analysis, if you don’t want to run a group-level analysis, you don’t necessarily have to normalize your images, which would save you effort and save your data from unnecessary interpolation.


Hi @Steven and thanks for your generously helping.

I mean do not want to run group-level analysis in FSL, I just need some preprocessed standardized images to perform some other analysis in other platform.

Is this correct:
flirt -in “preprocessedimage” -ref “T1image” -out “func2nativeimage” -init “example_func2highres.mat” -applyxfm
flirt -in “func2nativeimage” -ref “Standradimage” -out “func2native2standardimage” -init “highres2standard.mat” -applyxfm

If you have multiple transformations you want to apply, you can ConcatXFM as described in the user guide FLIRT/UserGuide - FslWiki

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