Re: [Freesurfer] Freesurfer Digest, Vol 206, Issue 6

What do you get if you run: cd /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/mri UpdateNeeded ../surf/autodet.gw.stats.lh.dat brain.finalsurfs.mgz wm.mgz ../surf/lh.orig.premesh

On 4/8/2021 5:59 PM, zalewk wrote:

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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:
>
> ????????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,

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*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 Send Freesurfer mailing list submissions to         freesurfer@nmr.mgh.harvard.edu

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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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