or start by sending us the recon-all.log from the two runs
On Fri, 8 Nov
2019, Chen, Christine wrote:
External Email - Use Caution
Hello,
My lab has been running T1 (MPRAGE) data through run_subject (uses recon-all,
autorecon, mris_volume
and mris_wm_volume) then through run.r (pulls freesurfer.r and pedbirn.r) using
the Desikan-Killiany
atlas to output measures of cortical morphology. We’ve always gotten consistent
output when
rerunning data, however, lately when rerunning data using the exact same files
as before, the output
measures are different, sometimes significantly so, compared to when they were
previously run.
We recently installed the development version of FreeSurfer in a path different
from
$FREESURFER_HOME, which is still set to usr/local/freesurfer. We’ve also
confirmed that all these
runs have been using FreeSurfer v6.0 by looking at the /scripts/build-stamp.txt
file. So the
inconsistency in output might not be due to the FreeSurfer version used.
Additionally, we are collecting a new dicom format, however when rerunning
files collected in the
previous dicom format through the pipeline and comparing this output to the
output from when it was
previously ran, the measures are still different, so the inconsistency in
results might not be due
to the dicom format.
Do you have any ideas why this sudden change in outputs is being observed? Is
there a flag we can
add to the scripts to ensure results are identical and consistent with what
they were previously,
such as –norandomness or –seed 1234?
Any help or guidance would be greatly appreciated. Thank you in advance.
Best,
CC
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