Hi, I have experienced this problem before also.So I have downloaded the script you provided but as a non-programmer I am wondering how I can incorporate this script into my work using Linux. Can I simply copy and paste this into the text editer and run it that way?
Thanks, Deirdre On Fri, Dec 14, 2012 at 4:37 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > it doesn't, although the 5.2 mri_normalize should help as well > > cheers > Bruce > > On Fri, 14 Dec 2012, Jonathan Holt wrote: > > OK this is great. Does this require the latest version of Freesurfer? I >> see >> recon-all v 5.2, we're running Freesurfer 5.0.0 for reference >> On Dec 14, 2012, at 1:16 PM, Alex Hanganu wrote: >> >> I think Emily is talking about this one: >> >> ftp://surfer.nmr.mgh.harvard.**edu/pub/dist/freesurfer/misc/** >> allplatforms/<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/> >> >> a. >> >> >> Le 14/12/2012 12:59 PM, Jonathan Holt a écrit : >> Emily, >> This is good news, can I find or download this revised version >> somewhere? >> >> jon >> On Dec 14, 2012, at 11:37 AM, Emily Rogalski wrote: >> >> We ran into this issue frequently and found that it >> was resolved by using the revised recon -all script >> that alters the stage where control points are >> considered. >> >> Emily >> >> >> On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt >> <whats...@umich.edu> wrote: >> OK will do... I'll upload both versions, >> before and after recon-all ran. I am >> beginning to think it's an issue with >> the script that I am running... I'm >> looking at another brain and there are >> areas I did not touch at all where white >> matter voxels are being added or >> removed... >> >> >> On Dec 12, 2012, at 11:33 AM, Bruce >> Fischl wrote: >> >> > Hi Jon >> > >> > if you upload this subject we'll take >> a look >> > Bruce >> > >> > >> > On Wed, 12 Dec 2012, Jonathan Holt >> wrote: >> > >> >> I've had this happen a handful of >> times and I'm wondering what I can do >> about it. For reference using Freesurfer >> 5.0.0. >> >> >> >> Edited a brain and ran "recon-all >> -autorecon2 -autorecon3 -s subj_id" >> which completed without error. The >> resulting brain had chunks of missing >> auxiliary volume in areas that I had not >> touched at all. This is bizarre and I am >> not sure what to do about it. Images of >> said issue attached of both main and >> auxiliary volumes. >> >> >> >> >> > >> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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. >> >> >> >> > _______________________________________________ > 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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