Hello there FSL people.
I am new to FSL First. I am currently using first_flirt and run_first to
perform alignment and segmentation of subcortical structures, which I then
compute the volume of (nonzero voxels) using fls_stats.
I have scripted this whole process and everything seems to be working very
well. I have noticed, however, some of my T1-weighted images in native space
are not particularly straight (i.e. a bit twisted - not well aligned). I
understand that we transfer our image in native space to 152MNI, but
segmentation actually takes place on the image in native space.
My main question is whether images not well aligned in native space are
likely to have an effect on the integrity of the segmentation process? If it
is, does FSL have a programme to straighten up the images in native space.
Many Thanks,
Liam.
