Hi Bruce,I have sent the link for a problem subject via a private message. Please note since MS causes hypointense lesions in white matter I have used an algorithm that fills hypointense lesions in WM with median intensity of normal appearing WM.ThanksJamesOn Fri, Jul 11, 2014 at 11:19 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi James
if you upload a problem subject we will take a look (the whole subject dir please)
cheers
Bruce
On Fri, 11 Jul 2014, james pardon wrote:
Hi all,
On a few subjects with a specific pathology (MS) I cannot easily reconstruct temporal lobes.
I think this issue comes up quite regularly on the mailing list, and I have tried to trouble
shoot using control points, WM edits, even getting back to orig/001.mgz to correct areas that
may seem the culprit for breaking surface reconstruction. Some subjects have gone through 7-8
runs of recon-all with different edits but still the problem persists in a few subjects in my
study.
I have also tried to use -mprage and -3T flags along the way to allow more liberal control
point growing, despite an improvement in my results some of subjects still have very bad
surface constructions. I have attached two snapshots to this email and I am happy to upload
the complete subject folder if you need to take a look at them.
As far as the SNR is concerned, I have designed my study based on recommended Freesurfer
parameters a couple of years ago on 3T Siemens Trio with 32-channel receiver coil.
A huge thank you for your previous helps, and thanks in advance for helping me with this new
issue.
James
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