Hi Louis,
I would appreciate if I could get your feedback on this specific subject we are experiencing problems with.
Thanks James
On Tue, Jul 15, 2014 at 8:20 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi James
I did, and one of our RAs here is going to be looking into it. Louis (ccd) can give you more information
cheers Bruce
On Tue, 15 Jul 2014, james pardon wrote:
Hi Bruce,
I was wondering whether you have seen my email below?
Thanks so much
Cheers, James
On Sat, Jul 12, 2014 at 9:18 AM, james pardon james.pardon15@gmail.com wrote: 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.
Thanks James
On 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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