Yes, it is a longitudinal analysis.
I'm waiting for Martin's reply.
Thanks for your time.
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Saturday, May 7, 2016 4:12:51 PM To: Freesurfer support list Subject: Re: [Freesurfer] correcting defects
so this is a longitudinal analysis then? If they are really the same subject, which I'm still not sure about as I think there were big differences in ventricle size (although it's hard to be sure just looking at the average) then there was a dramatic failure of registration. Martin: which volumes would you want to confirm this one way or the other?
cheers Bruce
On Sat, 7 May 2016, Katarina Trojacanec wrote:
Hi Bruce,
I checked and it looks like all time points are from the same subject. The first lines of the recon-all.log confirm that. Please find attached the processing commands I used step-by-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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Saturday, May 7, 2016 4:18:52 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] correcting defects
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 tiff of one 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@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