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.pardo...@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 <fis...@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 >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >
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