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Hi Doug,
Sorry, I didn't explain it clearly. We are running recon-all on our MPRAGE anatomical data, which is collected at 0.75mm^3 (this is in the 7T scanner in Bay 2 of the Martinos Center). We are specifying recon-all to run using the 1mm MNI templates. In the same scan sessions as these MPRAGE data are collected, we also collect EPI data at 1.5mm^3. If we were to run recon-all at 2mm, the spatial transformation matrices we would eventually use to coregister our EPI data to MNI space would also be at 2mm, and thus we would lose information due to coregistering at a worse resolution than our EPI data was collected at (2mm vs 1.5mm). So we want to run recon-all at 1mm so as not to lose information when we later coregister the EPI data. This works for many of our participants without issues, but for a select few (5-10% of our subjects), recon-all just hangs indefinitely after producing only a handful of the outputs in the "surf" folder. This does not happen when we run recon-all at 2mm: all outputs complete. So we want to know what is causing this issue and if we can get recon-all to run successfully on these few subjects at 1mm.
Thanks for your help,
Mike
On Sun, Jun 20, 2021 at 10:45 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
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:
External Email - Use CautionHello,
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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