External Email - Use Caution
Hi,
I have been trying to process 7T images but for most of them, recon-all just never finishes. It seems like it just bugged at some point with no error messages. At first, I thought that it just needed more time, but once, I had them running for more than 5 days and they were still stuck (they all get stuck at different stages of the process).
For example, one get stuck at this stage:
After retessellation of defect 13 (v0=21576), euler #=-176 (455542,1350444,894726) : difference with theory (-214) = -38
CORRECTING DEFECT 14 (vertices=77947, convex hull=8486, v0=30684)
I have been using Freesurfer and recon-all before and this is the first time it has happened to me. Does someone have an idea how to solve this issue?
I am using a macbook pro with 2.6 GHz 6-Core Intel Core i7 and 64GB of RAM. Catalina 10.15.7
Thank you very much, Samuel Paré
What kind of 7T image is it? Often they have terrible bias fields. Have you looked at the images with the ?h.orig.nofix surfaces? Also, remember to send your recon-all.log files.
On 8/27/2021 10:43 AM, Samuel Paré wrote:
External Email - Use Caution
Hi,
I have been trying to process 7T images but for most of them, recon-all just never finishes. It seems like it just bugged at some point with no error messages. At first, I thought that it just needed more time, but once, I had them running for more than 5 days and they were still stuck (they all get stuck at different stages of the process).
For example, one get stuck at this stage:
After retessellation of defect 13 (v0=21576), euler #=-176 (455542,1350444,894726) : difference with theory (-214) = -38
CORRECTING DEFECT 14 (vertices=77947, convex hull=8486, v0=30684)
I have been using Freesurfer and recon-all before and this is the first time it has happened to me. Does someone have an idea how to solve this issue?
I am using a macbook pro with 2.6 GHz 6-Core Intel Core i7 and 64GB of RAM. Catalina 10.15.7
Thank you very much, Samuel Paré
-- *Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
That defect is about half the size of a normal surface model, so I don’t think it will complete successfully! Doug is right about the bias fields, both transmit and receive, so you usually have to at least do something on the acquisition end to get a good-enough image. I’ll include Jon Polimeni on the thread as he has a lot of experience with this, but we’ll need more information about how you are acquiring the data Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Friday, August 27, 2021 4:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem, recon-all never finishes (it gets stuck)
What kind of 7T image is it? Often they have terrible bias fields. Have you looked at the images with the ?h.orig.nofix surfaces? Also, remember to send your recon-all.log files. On 8/27/2021 10:43 AM, Samuel Paré wrote:
External Email - Use Caution Hi,
I have been trying to process 7T images but for most of them, recon-all just never finishes. It seems like it just bugged at some point with no error messages. At first, I thought that it just needed more time, but once, I had them running for more than 5 days and they were still stuck (they all get stuck at different stages of the process).
For example, one get stuck at this stage:
After retessellation of defect 13 (v0=21576), euler #=-176 (455542,1350444,894726) : difference with theory (-214) = -38
CORRECTING DEFECT 14 (vertices=77947, convex hull=8486, v0=30684)
I have been using Freesurfer and recon-all before and this is the first time it has happened to me. Does someone have an idea how to solve this issue?
I am using a macbook pro with 2.6 GHz 6-Core Intel Core i7 and 64GB of RAM. Catalina 10.15.7
Thank you very much, Samuel Paré
-- Samuel Paré, MSc Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal
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Douglas N. Greve -
Fischl, Bruce -
Samuel Paré