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
<mreu...@nmr.mgh.harvard.edu <mailto:mreu...@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
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A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
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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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