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?
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