I don’t know if recon-all will pass those flags in or not. Probably best to let Bruce take a look.
Peace, Matt. On 5/13/14, 7:36 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >Hi Emil > >I would need the entire subject dir plus the T2-space volume > >cheers >Bruce >On Tue, 13 May >2014, Emil H.J. Nijhuis wrote: > >> >> Dear Bruce & Matt, >> thank you for your help. >> >> @Bruce: I would be happy to send you the data, just let me know by >>e-mail which files you wo >> uld need. >> >> @Matt: Could you please specify the commands for the flags >>-nsigma_above and -nsigma_below a >> nd how you would rerun the pipeline? Also what values would be >>recommended? >> >> I did not find any manual/help files regarding the flags, so it would >>be helpful to document >> it. >> >> NB. I found another thread in the maillist which probably relates to >>the issue: https://mail >> .nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033550.html . >>However I could not >> verify this, due to expired dropbox files. >> >> Yours, >> >> Emil >> >> Probably Emil¹s current example would be best because it is failing in >> your recon-all setup. >> >> Matt. >> >> On 5/9/14, 9:31 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >> >> >Hi Matt >> > >> >if you can send me an example I'll try to find time to take a look >> >Bruce >> >On Fri, 9 >> >May 2014, Matt Glasser wrote: >> > >> >> Hi Bruce, >> >> >> >> For whatever reason, sometimes the T2w surface adjustment will be way >> >>off. >> >> Adjusting the -nsigma_above <#> -nsigma_below <#> even a little bit >>up >> >>and >> >> down can get it out of the minimum and make it work, so there might >>be a >> >> bug. >> >> >> >> Peace, >> >> >> >> Matt. >> >> >> >> From: "Emil H.J. Nijhuis" <emil.nijh...@gmail.com> >> >> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> >> Date: Friday, May 9, 2014 at 4:53 AM >> >> To: <freesurfer@nmr.mgh.harvard.edu> >> >> Subject: Re: [Freesurfer] problem with pial surface reconstruction >> >>using T1 >> >> (MPRAGE) and T2 (SPACE) weighted images >> >> >> >> Dear Bruce, >> >> >> >> thank you for your help. >> >> >> >> attached I have put an fslview, tkmedit screen-shot of the T2 image >>and >> >>a tk >> >> surfer image of lh.woT2.pial. >> >> >> >> It appears that without consideration of the T2 this effect does not >> >>happen. >> >> >> >> What would be your recommendation if I would like to keep using the >>T2 >> >>weigh >> >> ted image? >> >> >> >> Yours, >> >> Emil >> >> >> >> Hi Emil >> >> >> >> how do the surfaces look before you apply the T2 deformation? And >>how do >> >> they look visualized over the T2 instead of the T1? >> >> >> >> cheers >> >> Bruce >> >> >> >> On Thu, 8 May 2014, Emil H.J. Nijhuis wrote: >> >> >> >> Hi, >> >> >> >> I have been using Freesurfer v5.3 to perform surface reconstruct for >>1mm >> >> isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens >>3T >> >>Trio >> >> scanner with a 32-channel head coil. Unfortunately for half of my >> >>subjects I >> >> receive an rather odd pial surface artefact, while the 'white' >>surfaces >> >>do >> >> not suffer from the same issue. >> >> >> >> The command line I have used was: >> >> >> >> recon-all -all -subjid <subjectid> -T2 <subjectdir>/mri/orig/T2.mgz >> >>-T2pial >> >> -3T >> >> >> >> Are you familiar with this issue and do you have some advice for me? >> >> >> >> Thank you very much for your help. >> >> >> >> Yours sincerely, >> >> >> >> Emil >> >> >> >> -- >> >> ---------------------------------------------- >> >> Emil H.J. Nijhuis, PhD >> >> Researcher - Division of Diagnostic and Interventional Neuroradiology >> >> University Hospital Basel >> >> Petersgraben 4 >> >> CH 4031 Basel Switzerland >> >> >> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> >> >>>>freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/ >>>>li >> >>sti >> >> nfo/freesurfer >> >> _______________________________________________ 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 . 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