It should just run the fill step. However, I've been slowly
reprogramming recon-all to just see what needs to be run and rerun it,
so you might get more than just the fill.
On 5/3/2024 4:38 PM, Dong, Yilei wrote:
External Email - Use Caution
Hi Freesurfer Developers,
Just to reply to this thread again, if I want to see if recon-all will
just run the -fill step, do I submit it on the files that have already
been run? In addition, does this error count as Freesurfer running out
of RAM or it's more of a cluster issue I have to talk with the staff
that manage it?
Sincerely,
Yilei
------------------------------------------------------------------------
*From:* Dong, Yilei <yid...@health.ucsd.edu>
*Sent:* Tuesday, April 23, 2024 3:34 PM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] recon-all process still not finishing
properly
Hi Freesurfer support,
I have several questions regarding recon-all -fill and -debug.
If we run recon-all -fill, what is the command set-up for that? From
the ReconAllDevTable here, *MailScanner has detected a possible fraud
attempt from "secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
<https://secure-web.cisco.com/1lmfyKn6Pvakq-RQxgJbE5k4RDGG6d0Vpvb5lGcjzph3h7UE3rIOK94h4_vGK8oa4q_FYtrbTmYfXg9SF-sFCkj4DY_oUkqnlqG_VRr6zv-uPviunfO901Vr4Llra2RZoL7k2SaVz5b8sHZwz9tr28nK4K01ItC1QwtyMTw-gA6LKU-lK3jTTjAHXqq0NK-7yqLmD6TCtsqdbNsdoxGLEfnWyV4rlB4ypTtbp8RQCkTKa8EWWLysYONW6-m24iLcIBbOt0l9i4UxjEV-DHag-8gIkxA9SeCthGdnNmHPEyy8ngikQbSR5ckvogYu-nsAi/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllDevTable>,
do we structure the recon-all command to be: recon-all -autorecon2
-fill -subjid <subjid>? I attempted to run recon-all -fill with -debug
with the structure as follows: recon-all -s $subject -i $1 -fill
-debug and I was wondering if this was the wrong format. I have also
attached our recon-all-slurm-apr19.sb cluster submission file for
reference.
Does recon-all -fill only run the fill step, while ignoring the
previous steps before that or does recon-all run through all the
initial steps including the -fill step ideally?
Regarding recon-all -debug, does the stdout file have the huge amounts
of text specifying what each line is doing? I have included .out and
.err files from the same recon-all -fill with -debug command for
reference.
Sincerely,
Yilei
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* Thursday, April 18, 2024 2:57 PM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] recon-all process still not finishing
properly
not sure what is happening. You can run recon-all with -debug and
capture the output (both stdout and stderr) into a file. This will
cause it to print out huge amounts of text specifying what it is doing
on each line. You should also see if there is some stderr output that
is not being caught. You can try running recon-all -fill on the
subject that you created to see if the fill will run at all (this may
be easier than waiting 4 hours).
On 4/8/2024 3:18 PM, Dong, Yilei wrote:
External Email - Use Caution
Hi Freesurfer Support,
The past few weeks, I've emailed about my recon-all processing stream
never completely finishing.
We are still encountering the same problem. For context, our
recon-all job submission script runs recon-all for 1 image. Given a
folder of 100 MRI images, we have another script that calls upon the
recon-all script for each image within the folder via a for loop. The
result is 100 jobs running in parallel on the cluster.
I have attached a screenshot of the parameters we set whenever we
submit each recon-all job for each image by SLURM to UCSD's cluster.
The maximum time we are allowed for each job is 48 hours. Our jobs
are shared-node jobs, which means we run more than 1 job on a single
node. This time, we increased RAM from 8GB to 16GB in hopes the
entire recon-all processing stream can fully run through for each
image, but it still stops at "mri_pretess done" and does not go on to
the -fill step. Each job submitted to the cluster took around 4 hours
and 20 minutes each to run in our most recent attempt.
If increasing the RAM did not change anything for us, how else can we
get more verbose error messages? What other reasons could be why our
recon-all aborts before finishing? I have attached a recon-all.log
from one of our subjects for reference and a screenshot of the
parameters we set for submitting jobs in our cluster for reference.
Freesurfer version: 7.2.0, but already available as module on UCSD's
cluster system
Platform: Rocky Linux release 8.8 (Green Obsidian)
uname -a: Linux login01 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun
28 15:04:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
Recon-all log: see attached
Thank you!
Sincerely,
Yilei
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