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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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