I preprocessed my fMRI data with fMRIprep without ICA-AROMA. To do the further analysis, I want to smooth the image with 4mm FWHM. How should I do?
In FSL, smoothing is processed by susan command. I read through the manul of susan in fsl wiki, however, it is still hard for me to know how to define the bright threshold. any suggestions will be greatly appreciated.
I’m not very familiar with SUSAN, but fMRIPrep does run SUSAN when ICA-AROMA is enabled. The smoothed data aren’t retained or anything, but the settings used in that step are probably pretty good. Here is the relevant section of code:
Hi, everyone. After a hard effort of searching and asking, I think I have a cue about solving this problem now.
Through an answer in FSL-mail-list, the bright threshold is set by 0.75 multiply the contrast between median brain intensity and backgroud. Then, referencing the log report of FSL Feat, the Susan smoothing could be proceeded as follows:
The result in step 3 multiply 0.75 is the bright threshold that we are after (326.02 * 0.75 = 244.51). The FWHM I used is 4 mm, given that the voxel of my data is 2.4 mm^3.
susan <pre_thr_func_img> 244.51 1.698 3 1 1 <mean_func> 326.02 <pre_thr_func_img_smooth>
That’s it! We could get the image with 4mm-FWHM smoothing, and the iamge seems OK by visual inspection. I am not so prefessional to FSL, so I don’t know if it is a proper way to use susan. Please let me konw if this pipeline has any mistakes.
Thank you QunjunLIANG for sharing this. I’ve been trying to replicate/understand steps in the Feat pre-processing pipeline and this resolves the origin of some magic numbers that popped up in their log files.