5 Apr
2016
5 Apr
'16
4:41 p.m.
Hi Mihaela,
you can use our BrainPrint tool (after running FS) to see how closely the brain shape matches:
http://reuter.mit.edu/publications/pid/wachinger-brainprint15 http://reuter.mit.edu/software/brainprint/
Best, Martin
On 04/05/2016 12:49 PM, Mihaela Stefan wrote:
Hi Martin, Just an update on this. It turned out that there was just a DICOM mismatch for this subject but now that you mentioned it, I wonder what people do to make sure that the same person returns for follow-up in a longitudinal study. Even when there is one study coordinator for the entire length of the study, it's quite difficult for that person to remember hundred of faces and asking for an ID is not always doable.
Thanks! Mihaela
On Thu, Mar 31, 2016 at 1:50 PM, Mihaela Stefan <mikaelastephan@gmail.com mailto:mikaelastephan@gmail.com> wrote:
Wow! I haven't thought about that but it's possible since we had a few study coordinators along the way. So it could be the case that the study coordinator didn't know the subject who came at follow-up. Hopefully it will be just a DICOM mismatch. Will see how it goes.. :) On Thu, Mar 31, 2016 at 10:38 AM, Martin Reuter <mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> wrote: I have seen cases where annonymization messed up ID's and individual time points came from a different subject. That could mess things up quite bad. (Also if the person sends their sibling or friend, because they don't have time to come to the follow up themselves, has also happened - not to me though ). Best, Martin On 03/31/2016 10:21 AM, Mihaela Stefan wrote:Hi Martin, We ran this subject twice but we got the same error. The norm is not aligned. They almost look like two different brains. I double checked the exam numbers to make sure that these three exams belong to the same person. They indeed seem to belong to the same person but I will re-run recon cross from scratch for MRI3 just to make sure that I started with the right DICOMs. I will let you know how it worked. Thanks! Mihaela On Wed, Mar 30, 2016 at 4:12 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> wrote: Hi Mihaela, does the cross sectional run of that time point, and the base look OK? Also check if this time point is aligned correctly to the base (e.g. open norm.mgz from the long and the base, they should be aligned). If all this is OK, then I would recommend to re-run this long run again, but make sure you are removing the longitudinal directory first so that it re-runs from scratch. If that does not fix it, we would need to get the data for debugging. Thanks, Martin On 03/30/2016 03:19 PM, Mihaela Stefan wrote:Dear FreeSurfers, We are doing a longitudinal analysis with three time points (MRI1, MRI2, MRI3). All the subjects were processed well except for one. The MRI3.long of that subject has very bad surfaces (see attachment - I am also attaching the log file). The cross, the template and the first two long runs were reconned well, though. We can't figure out why this third run is so bad. As a note, we processed all the cross runs on an Ubuntu machine but we ran the longitudinal pipeline on a computer cluster (both with freesurfer v5.3). We ran the long twice for that subject thinking that the pipeline crashed somehow the first time. However, the results were the same. Any help would be appreciated. Thanks! Mihaela _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> Web :http://reuter.mit.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> Web :http://reuter.mit.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web : http://reuter.mit.edu