Hi Bruce, I already double checked and it looks like all time points are from the same subject. Please find attached the processing commands I used step-by-step (the same I sent you in the previous mail about this question).
Do you need some more detailed information? Cheers. Katarina 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: Saturday, May 7, 2016 4:03:28 AM To: Freesurfer support list Subject: Re: [Freesurfer] Correcting defect Hi Katarina how did you create the orig.mgz for these subjects? Either some registration failed badly or you tried to average data from different subjects (see attached tiffs of the orig.mgz you uploaded) cheers Bruce On Thu, 5 May 2016, Katarina Trojacanec wrote: > Hi Bruce, > > I uploaded the subject dirs (base for TP1_4 and TP2_4, as well as the > cross-sectionally processed time points for TP1, TP2, and TP4). In the > meantime, one of them, template TP1_4 has finished with error. The other one > (base TP2_4) is still running. > > What do you suggest in this situation. > > Sorry for the inconvenience. > > 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: Thursday, May 5, 2016 4:20:31 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Correcting defect > > 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. > > > _______________________________________________ > 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
