Thank you so much! Mihaela On Tue, Apr 5, 2016 at 4:41 PM, Martin Reuter <[email protected]> wrote:
> 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 <[email protected]> > 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 < >> <[email protected]>[email protected]> 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 < >>> <[email protected]>[email protected]> 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 >>>> [email protected]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 >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> [email protected] >>>> 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 >>> [email protected]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 >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> [email protected] >>> 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 > [email protected]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 > > > _______________________________________________ > Freesurfer mailing list > [email protected] > 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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