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 would need. @Matt: Could you please specify the commands for the flags -nsigma_above and -nsigma_below and 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 . 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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