Hi Pedro
if you are able to change the acquisition in the future you might try
something closer to isotropic, which would let you get the echo time
down. Longer TE decreases contrast as it allows some T2* weighting (which
is in the opposite contrast direction to T1) to creep in.
cheers
Bruce
On Wed, 8 Apr 2015, Pedro Rosa - Gmail wrote:
Hi,
Thanks a lot, Bruce. These are from a 1.5T GE Signa scanner, with a T1-SPGR
sequence with 0.86x0.86x1.5mm voxel size, echo time 5.2ms, resolution time
21.7ms, flip angle 20. This is an older sample we have, and I intent to
replicate earlier SPM analyses but now using FreeSurfer. I acknowledge the
low contrast problem, but I am having success in correcting topological
errors in the temporal lobe, and only these insula problems show to be
harder to deal with.
Your help will be very appreciated! I am now putting the file
(PedroRosa.zip)
Best,,
Pedro Rosa
On Tuesday, April 7, 2015 at 9:29 AM, Bruce Fischl wrote:
sure, upload it and we will take a look. Can you tell us a bit
about the
acquisition? It's hard to tell for sure with the parcellation
overlaid,
but it looks *very* low contrast, which I'm sure is making things
harder
cheers
Bruce
On Mon, 6 Apr 2015, Pedro Rosa - Gmail
wrote:
Dear FreeSurfers,
I was correcting the topology of some subjects, and could not
fix some subjects whose insula is misplaced into the temporal
lobe / subcortical regions. Inspecting wm.mgz in tkmedit, it
seems that there are wm voxels into the hippocampus, perhaps
leading surfaces to be built there. Removing them, however, did
not help (actually, it seems that it made things worse). Can you
help me? I can upload the subject if it you think it is
suitable.
Many thanks in advance,
Pedro Rosa.
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