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Hi Doug,
Sorry for the late reply, and thanks for all your help. Attached is the text file of the output. This was testing autorecon-pial, but the bug is the same no matter if it's autorecon2-wm, autorecon3, or any place it hits the "if ( $ud" statement.
Best, Kody Run it with -debug as the first option, capture the output, and send it to us. On 4/1/2021 8:29 PM, zalewk wrote:
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Hi Freesurfer team,
My lab recently switched over from FS6 to FS7 and I think I've encountered a bug with recon-all. I'm running subjects stepwise and editing them, running recon-all with the -autorecon2 and -autorecon3 flags initially are no problem, they run fine.? Trying to re-run them or use the -autorecon2-wm, -autorecon-pial etc. flags lead to crashing at certain parts of the program. The error message I get is "if: expression syntax". Digging into the code, it seems to crash when it hits a line of code "if($ud || $ForceUpdate)". The syntax superficially looks right (I don't know tcsh), checking the variables it seems like $ForceUpdate is never set, but removing it from recon-all doesn't fix the problem. It seems the $ud variable is for checking if updates are needed for a set of volumes passed to the program. I don't know why that would be a problematic argument, removing that part seems to fix it, but this also seems like an important variable and I don't know enough about tcsh to understand why it works after removing it. Can one of the folks who wrote the recon-all script help me out? I'm running the commands step-wise as a work-around, but that is much less convenient.
Best,
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu freesurfer-request@nmr.mgh.harvard.edu Sent: Tuesday, April 6, 2021 6:41 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 206, Issue 6
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Today's Topics:
1. Freesurfer Website Ports (Swearingen, Hannah) 2. mris_average_surface fails (?????????) 3. Re: 2mm thick image for hippocampal segmentation. (Ramesh Babu) 4. Re: fMRIPrep BOLD Output (Douglas N. Greve) 5. Re: mri_glmfit error (Douglas N. Greve) 6. Re: Regarding recon all (Douglas N. Greve) 7. Re: retaining label ids (Douglas N. Greve) 8. Re: recon-all bug (Douglas N. Greve) 9. Re: mris_label2annot - make all command exiting with errors (Douglas N. Greve) 10. Re: recon-all bug (Douglas N. Greve) 11. Re: Dicom Tag Problem Reconall (Douglas N. Greve) 12. unsubscribe (Coleman, Katherine) 13. Re: mri_gtmpvc error Checking tissue type ERROR: CheckSegTissueType() tissue type for seg (Douglas N. Greve) 14. Re: Problem with freesurfer measures (Douglas N. Greve) 15. Re: Freesurfer Website Ports (Douglas N. Greve) 16. Re: mris_average_surface fails (Douglas N. Greve) 17. Re: 2mm thick image for hippocampal segmentation. (Douglas N. Greve) 18. Freesurfer Versions - Zeros in the Cortex (Daniel Gutstein) 19. Re: mri_gtmpvc error Checking tissue type ERROR: CheckSegTissueType() tissue type for seg (Bahar Hazal Yal??nkaya)
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Message: 1 Date: Mon, 5 Apr 2021 15:20:31 -0400 From: "Swearingen, Hannah" hannah_swearingen1@brown.edu Subject: [Freesurfer] Freesurfer Website Ports To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAG+grQp1wJ8ywX0StrT4VJO38JYtwfxivTNvdH3KwQrhtwiRGw@mail.gmail.com Content-Type: text/plain; charset="utf-8"
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Hi,
I am setting up an Access Control List for an isolated VLAN in which my center's neuroimaging computing workstations will be connected to our hospital's network for data back-up.
We want to be able to connect to Freesurfer's website while connected to the VLAN, and we need to supply which ports the website accesses. I used nmap to scan and see which ports are open, and I found this:
PORT STATE SERVICE
21/tcp open ftp
80/tcp open http
443/tcp open https
Our hospital's IT is unsure if the FTP port can be opened without a security breach, and they are wondering if we will still be able to access the website without the 21/FTP port opened?
Can anyone provide me with that information?
Thanks,
Hannah
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