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 laurasvanvelzen@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