New subject: Freesurfer Digest, Vol 206, Issue 6

8 Apr 2021


      External Email - Use Caution
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 ( $ud" statement.
Best,
Kody
Run it with -debug as the first option, capture the output, and send it
to us.
On 4/1/2021 8:29 PM, zalewk wrote:
...
????????External Email - Use Caution
Hi Freesurfer team,
My lab recently switched over from FS6 to FS7 and I think I've
encountered a bug with recon-all.
I'm running subjects stepwise and editing them, running recon-all with
the -autorecon2 and -autorecon3 flags initially are no problem, they
run fine.? Trying to re-run them or use the -autorecon2-wm,
-autorecon-pial etc. flags lead to crashing at certain parts of the
program. The error message I get is "if: expression syntax". Digging
into the code, it seems to crash when it hits a line of code "if($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)
----------------------------------------------------------------------
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"
External Email - Use Caution
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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Re: [Freesurfer] Freesurfer Digest, Vol 206, Issue 6