Hi Katarina if you want us to look you need to upload the entire subject dirs (tarred and gzipped). TO visualize it, look at the inflated.nofix in freeview in 3D mode and just see what the big defects look like. If you load the orig.nofix at the same time you can goto a vertex in the big defect you see on the inflated by typing its index into the info winwo for the orig.nofix. This will be automated in v6
Bruce On Thu, 5 May 2016, Katarina Trojacanec wrote: > Thank you. > I have uploaded the files (lh.inflated_TP_1_4.nofix and > lh.inflated_TP_2_4.nofix). > > What should I do as a next step? > > Cheers > Katarina Trojacanec, M.Sc. > Teaching and research assistant > > Faculty of Computer Science and Engineering > Ss. Cyril and Methodius University - Skopje, Republic of Macedonia > > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl > <fis...@nmr.mgh.harvard.edu> > Sent: Wednesday, May 4, 2016 2:35 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Correcting defect > > sure. Or you can load the ?h.inflated.nofix and look at it - it should be > obvious if there is a huge defect (you can also load the file > ?h.defect_labels as an overlay on that surface and it will show you the > segmentation of the defects) > > cheers > Bruce > On Wed, 4 May 2016, Katarina Trojacanec wrote: > >> >> Dear FreeSurfer Team, >> >> >> I have been trying to run creation of template with FreeSurfer. However, >> for two cases for one patient (case 1: template based on TP1 and TP4, case >> 2: template based on TP2 and TP4), the correcting defect step is running >> too long. According to the information in the mail archive, the defects are >> probably too big, and that is the reason for the long processing. >> >> >> May I send you via ftp the subjects directories so you can help me to >> proceed with this subject, because I am not able to figure out and correct >> the problem? Should I send you the base directories in their current state >> or the cross-sectionally processed time points as well? >> >> >> Best Regards, >> >> >> Katarina Trojacanec, M.Sc. >> Teaching and research assistant >> >> Faculty of Computer Science and Engineering >> Ss. Cyril and Methodius University - Skopje, Republic of Macedonia >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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.
