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Dear sir/madam,
Being interested in improving the pial surface construction in our datasets (acquired at 3 Tesla), I have been considering the addition of the T2-weighted image from our studies' protocol to our recon-all run. However, looking at its acquisition parameters, I'm sure as to whether making use of this T2-weighted image would benefit pial surface construction. First, some parameters:
T1-weighted image: 3D sagittal spoiled-gradient FFE TR/TE: 10.02/4.6 FA: 8 Slices: 200 .75x.75x.8 mm³
T2-weighted image: Dual Echo - TSE clinical scan transversal T2-weighted TR/TE: 600/80 FA: 90 17 slices of 5 mm slicegap: 1.2 mm
And our initial recon-all run, without the T2-weighted image: recon-all -all -i sub -subjid subid -3T -hires -expert expert.opts The recon-all run I had in mind with the T2-weighted image added: recon-all -all -i sub -subjid subid -3T -hires -expert expert.opts -T2/path/to/T2 -T2pial expert.opts content: mris_inflate -n 50
Now, my question is, would a T2-weighted image acquired at the abovementioned parameters actually do the pial surface construction any good when included to a recon-all -hires run on submillimeter T1-weighted images like ours? Or, would it perhaps worsen pial surface construction, even (owing to, for example, the low resolution of the T2-weighted image)?
I have tested this on one of our subjects, which had a lot of dura included to the pial surface in the recon-all run without the addition of the T2-weighted image. After running recon-all on this subject again, this time with the T2-weighted image included and -T2pial turned on, (slightly) less dura was included to the pial surface (i.e., improvement; top two images for comparison example), but now it also seemed to exclude some parts of the cortex on other spots (bottom two images for comparison example), as well.
[cid:196242f0-e97c-43e8-b940-8843db62ab07] [cid:737f0df8-9a94-4b61-ac9f-a403d5389acf] dura inclusion comparison left: without -T2 and -T2pial right: with -T2 and -T2pial
and:
[cid:afefd874-e994-4b34-87fd-cef34040bdce] [cid:d7047b7f-d15f-424d-8f5e-1c9602a3f298] pial surface quality comparison in sulcus left: without -T2 and -T2pial right: with -T2 and -T2pial
I would greatly appreciate FreeSurfer experts' advice on this. Thank you very much for your time!
Kind regards, Simon Poortman (Erasmus MC, Rotterdam)
