Do I understand correctly that you are running recon-all with EPI data?
If so, that will certainly not work.
On 6/11/2021 11:46 AM, Michael Datko wrote:
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Hello,
I have been collecting data on a 7T scanner, with functional EPI data
collected with 1.5mm voxels, and I have been having an issue with some
of our data where recon-all just hangs after producing only a small
amount of outputs. For instance, it might get to a point where it has
generated 5-10 of the “lh” left hemisphere outputs in the surf folder,
and then appears as if it continues to run for hours or days but no
other outputs get produced and eventually the process times out and
quits. I estimate that this happens for about 5-10% of the
participants we have collected so far. If it doesn’t work for a
particular participant, it will do the same thing again if I delete
their temporary working folder and any outputs and try to run again
from scratch.
This is not happening with data from the same participants collected
from a 3T scanner with 3mm EPI voxels, with recon-all run at 2mm. The
only difference is the resolution of the data and therefore the
resolution at which we are running recon-all. Our 7T functional EPI
data is collected at 1.5mm resolution, so for those scans we run
recon-all at 1mm resolution.
Do you have any advice for how to get these participant’s data to
finish with recon-all at 1mm?
Thank you,
Mike Datko
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