I’ve been tasked with finding subcortical hippocampal, putamen and thalamus volume using 160 subject T1s.
I have run all the T1s through First (after visually inspecting the T1s, checked potential errors using (e.g. cat subject01.logs/*.e*)
and checked registrations using ${FSLDIR}/bin/slicesdir -p ${FSLDIR}/data/standard/MNI152_T1_1mm.nii.gz *_to_std_sub.nii.gz. No errors were detected.
However, I’d also like to verify for each *_all_fast_firstseg.nii.gz segmentation that the amygdala is not a substantive part
of the hippocampus; that the pallidum is not as substantive part of putamen - in 3 or more slices.
Question 1.
Viewing the all_fast_firstseg.nii.gz image for each subject in fsleyes provides one level of visual segmentation inspection.
The all_fast_firtseg image is in (corrected) native space; perhaps using flirt to create a transforming mask from native to standard space might be of use as well? Please advise
Question 2.
“Substantive part” is of course vague. Any recommendation specifying the number of overlapping voxels(e.g. between hippocampus and
amygdala)that suggest segmentation failure (likely due to a problem with the T1) would be greatly appreciated.
Best,
Lance
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