Low intensity T1 FreeSurfer

Hi everyone,
I have some T1 images that show reduced intensity (or signal loss) in dorsal cortical areas, and those regions are therefore cut off when FreeSurfer is used for cortical segmentation (see example). Does anyone have a suggestion on how to correct for this signal drop-out somehow before running FreeSurfer or if it is possible to change settings in FreeSurfer to make it more sensitive to pick up on these lower signals?

Hi Yara, I have the same problem in the same area and I’m therefore wondering if you might have found a solution for this yet? Thank you in advance.

@Yara and @JuliaLam You could look at using control points: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPointsV6.0 they aren’t exactly meant for fixing this problem, but you may be able to jerry rig a solution out of them.

Might also help to know what exactly caused the low intensity in the first place

Hi @BradleyHuff,
Thank you for your respons. I tried control points but quickly realized it would require adding many control points across many slices in nearly all the subjects. Unfortunately, I do not know what exactly caused the the low intensity. However, we found that the intensity in T1 sag was better than in the T1 tra ones. So I am currently running recon-all on sag to see if segmentation is improved. :slight_smile: