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> 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


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-- 
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

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