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Hi,
I have been looking to use SAMSEG to segment T1 and FLAIR images and then feed the segmentation results into the recon-all pipeline. The command I have been using is below:-
/Applications/freesurfer/bin/samseg --t1w ./T1/Subjects/MP074.nii.gz --flair ./FLAIR/Subjects/MP074.nii.gz --hires --use-flair --normalization2 --fill --pallidum-separate --threads 4 --s MP074 --recon --refmode t1w
The job completes without error and the segmentations look fine but when I look at the FLAIR images then images in the coreg and input folders in the subject directory are fine but when I look at the images in the mri directory while the FLAIR.prenorm.mgz looks fine the FLAIR.norm.mgz and FLAIR.mgz images are normalized T1 images with some of the neck clipped off and are indistinguishable from the nu.mgz image. The SAMSEG segmentation isn't affected since it uses the FLAIR image from the coreg directory but I'm assuming the issus with the FLAIr.norm and FLAIR images will have repercussions for the rest of the recon-all pipeline since I'm using the -use-flair option. Is that correct and is there a fix for this?
I'm using a Mac Pro running version 12.6.8 (Monterey) of the Mc OS. I'm running version 7.4.0 of the Freesurfer software. I have attached the logfile and a pdf file showing some of the images.
Richard