Hi Laura, it could be that 9 years of severe aging or neundegenerative disease are too far apart for the method to cover the distance. The base would look blurry or show ghosting (in 2 time points the median is equal to the mean and the mean will not look good with too much change). I would recommend to do your analysis only with the cross sectional stream until you get at least one more time point for this data.
Best, Martin > On 10. May 2018, at 07:12, Laura van Velzen <laurasvanvel...@gmail.com> wrote: > > > Dear FreeSurfer experts, > > We are trying to run FreeSurfer v5.3 on our longitudinal imaging data using > the longitudinal pipeline. We first processed both time points > cross-sectionally. The output of this step looks fine for both time points. > > We then performed step 2: creation of a template from both time points and > step 3: longitudinally processing both time points. All steps run without > errors, but the output of steps 2 and 3 look abnormal (please see images > attached), so there appears to be something wrong in the creation of the > template. We also have some subjects with data from only one timepoint and > ran the longitudinal pipeline for these subjects as well (as was recommended > on the wiki) and the output of steps 2 and 3 look fine for these subjects, so > there appears to be an issue in creating the template based on both time > points. > > The acquisition parameters at both time points are the same as far as we > know. There is nine years between both measurements, and most of our subjects > are between 50 and 60 years old at the second measurement. > > We have attached the recon.all.log file for one of our subjects. > > We hope you have some suggestions what the problem might be and how we could > check this. > > Many thanks in advance for your help! > Kind regards, > > Laura van Velzen & Julia Binnewies > <Example 2.zip>_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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