Glad to hear!
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Abigail Waters [awaters2@suffolk.edu] Sent: Tuesday, February 21, 2017 7:31 PM To: Freesurfer support list Subject: Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
Hi - So I went ahead an uninstalled and then reinstalled the update to see if that fixed the problem, and it seems to be working fine now. Thank you for your help! Best Abby ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edu] Sent: Wednesday, February 15, 2017 4:57 PM To: Freesurfer support list Subject: Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
Hi Abby – Interesting, this means that it was the update and not the subject. I’ve never seen this issue before, and unfortunately these are all old builds that are hard to troubleshoot now. But if you want to send me one of the subject’s TRACULA directories, I can try to replicate the error on a mac here or see if a new build would fix it.
https://gate.nmr.mgh.harvard.edu/filedrop2/
On a side note, it’s also fine if you’ve run recon-all from FS 5.3 and then run trac-all from FS 6.0, as long as it’s done consistently across all subjects in your study.
Best, a.y
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Abigail Waters <awaters2@suffolk.edumailto:awaters2@suffolk.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, February 15, 2017 at 2:34 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
Hi - Sorry about that! I was not aware that anything had been updated and was only checking the freesurfer version in the log. The previously successful subject failed, I've attached the log. Thanks! Abby ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu] Sent: Tuesday, February 14, 2017 5:07 PM To: Freesurfer support list Subject: Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
Hi Abby – It looks like the first subject was run before installing the 2014 TRACULA update, and the second subject was run after installing that update. Can you try running the first subject from scratch (in a new output directory) now that the update has been installed? This will tell us if it’s a difference pre and post update, or a difference between the 2 subjects.
Thanks, a.y
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Abigail Waters <awaters2@suffolk.edumailto:awaters2@suffolk.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, February 14, 2017 at 2:55 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
Attached are both the successful and failed trac-all logs. ________________________________ From:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu] Sent: Monday, February 13, 2017 3:03 PM To: Freesurfer support list Subject: Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
That's very strange, it sounds like nothing has changed. Can you please send your trac-all.log file?
________________________________ From:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Abigail Waters [awaters2@suffolk.edumailto:awaters2@suffolk.edu] Sent: Monday, February 13, 2017 2:29 PM To: Freesurfer support list Subject: Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
It's the same. These are all subjects from the same research protocol. ________________________________ From:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu] Sent: Sunday, February 12, 2017 9:39 PM To: Freesurfer support list Subject: Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
Is the data size different for the new subjects than the old subject? Is the spatial resolution or number of directions higher? Or is the acquisition exactly the same?
________________________________ From:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Abigail Waters [awaters2@suffolk.edumailto:awaters2@suffolk.edu] Sent: Friday, February 10, 2017 8:37 PM To: Freesurfer support list Subject: Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
The successfully processed subject was completed using the same FS version (5.3) in December. We have not updated to FS 6. The only thing that was altered was the directory structure in the dmrirc text file, and the subjects. Thanks! Best Abby ________________________________ From:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu] Sent: Friday, February 10, 2017 4:34 PM To: Freesurfer support list Subject: Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
Hi Abby – When you say you have successfully processed a subject on that machine before, what FS version was that with? What has changed since then? The last I remember memory allocation issues, they were years ago in a very old version of OSX that we don’t even distribute binaries for any more, so I don’t think this is the same problem.
Best, a.y
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Abigail Waters <awaters2@suffolk.edumailto:awaters2@suffolk.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, February 10, 2017 at 3:05 PM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
Hello - I'm attempting to run the -trac-all -prep command with FS 5.3. I am running into the same memory allocation issues on my Mac that were present in earlier versions of Freesurfer/Tracula. See below:
MRIallocSequence (218, 182, 1):could not allocate 158784 bytes for the 44th slice Cannot allocate memory
I have attempted the pre-processing with multiple and single subjects. I have successfully processed a single subject on this machine before, and have not updated to the latest Freesurfer since that subject (as all MPRAGE scans were reconstructed is FS 5.3). There is sufficient memory available and the MPRAGE scans were reconstructed correctly.
Any thoughts on how to solve the issue would be appreciated. Please let me know if you need any additional information. Thanks! Abby