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Hi Freesurfer team,
Please can I run the parallel Command for freesurfer? I am using windows
11.
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>
>
> Yujing
>
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *P Pieperhoff
> *Sent:* Wednesday, November 8, 2023 5:28 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesur
the tasks and run them in parallel. They are the
same flags.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of P Pieperhoff
Sent: Wednesday, November 8, 2023 5:28 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] parallel processing of long-run fails
Ex
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I'm not sure the parallel flag works any more. But you can specify
multiple threads with -threads N
On 4/27/2023 5:45 AM, Michael Mc Laughlin wrote:
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That is a single command. How can you run a single command in
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Thanks for pointing that out, sir.
2023年4月27日(木) 16:15 Toshiharu Kamishikiryo :
> Hello Freesurfer experts
>
> I am trying to recon-all using T2 images as well to improve pial
> surfaces. Does anyone know how to use GNU Parallel in bash to run the
> f
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That is a single command. How can you run a single command in parallel?
You can add the -parallel flag to get freesurfer to run recon-all in
parallel threads.
On Thu, Apr 27, 2023 at 8:16 AM Toshiharu Kamishikiryo
wrote:
> External Email -
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Hello Freesurfer experts
I am trying to recon-all using T2 images as well to improve pial
surfaces. Does anyone know how to use GNU Parallel in bash to run the
following commands in parallel?
recon-all -subject subjectname -i /path/to/T1w.nii -T2 /pat
There is not an easy way to do this. Internally, there is a binary that
loads all the subjects then creates an average. You need some way to
create intermediate files, then combine them together, which we don't
support. Why do you want to create an average subject?
On 4/11/2022 9:54 AM, Marina
3
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] parallel make_average_subject
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Dear experts,
I would like to create an average subject from a very large population. I am
going to compute it on a computer with a lot of threads and I would like to
know if i
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Dear experts,
I would like to create an average subject from a very large population. I
am going to compute it on a computer with a lot of threads and I would like
to know if it is possible to parallelize the make_average_subject function
to try to sho
If you are using slurm, then you have to allocate the number of CPUs
when you run sbatch, otherwise, you will get only one CPU regardless of
how many are tell recon-all to use.
On 1/29/2021 1:16 PM, Wei Shao wrote:
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Hi, Freesufer experts
Sorry for the lat
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Hi, Freesufer experts
Sorry for the late reply, I have tried again with openmp 8 flag and added
the cpus-per-task=16 for a subject. I have cut the recon-all processing
time from 06:17:14 to 03:32:21! So excited.
By the way, Could you help me to unders
No, all the results are fine. By "broken" I mean that it might crash in
places that it would not have crashed in v6 or that it just would not
have been running in parallel when you think it was.
On 1/28/2021 3:48 PM, Michael Krause wrote:
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>
> On 1/28/21 6:
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On 1/28/21 6:00 PM, Douglas N. Greve wrote:
> No, use of -threads or -openmp will always trigger the openmp code. The
> -parallel may introduce other parallel. I did not write this part of the
> code so I'm not sure, and I think I might have broken th
No, use of -threads or -openmp will always trigger the openmp code. The
-parallel may introduce other parallel. I did not write this part of the
code so I'm not sure, and I think I might have broken the -parallel
implementation when I did the last recon-all rewrite
On 1/28/2021 11:23 AM, Michae
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> 1 According to documents, freesurfer is OpenMP code , I use -openmp 8
> flag like: recon-all -alli -i input.file -s output.file -openmp 8
> to tun the recon command on a server, but it doesn't work for me (the
> running time is very similar for the
On 1/27/2021 2:02 PM, Wei Shao wrote:
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Hi, Douglas
Thanks for your kind reply.
1 I run the same subject on a server with openmp 8 flags cost 7 hours,
without openmp 8 flag would be 7h10minutes.
Can you send the two recon-all.log files?
3 Could you be
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Hi, Douglas
Thanks for your kind reply.
1 I run the same subject on a server with openmp 8 flags cost 7 hours,
without openmp 8 flag would be 7h10minutes.
3 Could you be more specific about run them by hand? is this mean I run
different tasks like sk
On 1/20/2021 3:39 PM, Wei Shao wrote:
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Hi, Freesufer experts
My name is wei shao, I have a few questions regarding the
parallel computing of recon-all
1 According to documents, freesurfer is OpenMP code , I use -openmp 8
flag like: recon-all -alli -i i
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Hi, Freesufer experts
My name is wei shao, I have a few questions regarding the
parallel computing of recon-all
1 According to documents, freesurfer is OpenMP code , I use -openmp 8 flag
like: recon-all -alli -i input.file -s output.file -openmp 8
to
No, you are not overwriting anything.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of gunes
Sent: Monday, October 5, 2020 12:19 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Parallel Run of Multiple Patients
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Thank you for your response!
Yes, each patient has its own folder, but inside these patient specific
folders, there are symlink folders (namely fsaverage, lh.EC_average and
rh.EC_average) pointing to folders with the same name under
*$FREESURFER_HOME/s
No I don't think so. As long as each subject has its own name/folder,
there will not be any problem. We do this kind of thing all the time
with hundreds (or more) subjects running simultaneously.
On 10/5/2020 11:14 AM, gunes wrote:
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Dear Freesurfer expert
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Dear Freesurfer experts,
We have a pipeline script that uses *recon-all* and other executables
(like applywarp, mri_convert, mri_em_register etc.) several times. We ran
our script in parallel from different terminals to process the patients
faster. How
Hi John
so, you don't want to give recon-all multiple subjects. If you have
enough ram you should just call it once for each subject and not use the
openmp flag
cheers
Bruce
On Thu, 19 Jul 2018, John Absher wrote:
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We are trying to run many subj
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We are trying to run many subjects through recon-all in batches on an 8 core
Windows Server on which we have virtualBox running CentOS7 and freesurfer 6.
Can you tell me if this command will utilize all 8 cores effectively to process
all 8 subjects s
Hi Hassan
you can either run multiple instances of recon-all (if you have enough RAM
and CPUs), or you can use the -openmp flag to
parallelize a single instance.
cheers
Bruce
On Mon, 13 Apr 2015, Hassan bakhshi wrote:
> Hi,
> Is it possible to run recon-all in parallel for fastening the sp
Hi,
Is it possible to run recon-all in parallel for fastening the speed ???
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Dear Elijah,
If I'm right, there are two options to accelerate FS execution:
1) The first option is using the FS openmp implementation
http://surfer.nmr.mgh.harvard.edu/fswiki/OpenMP. I haven't tested this way
but openmp allows to open multiple processing threads, and it is supported
for the most
Hi FSL Experts,
I am currently processing a large dataset and would like to seek some
advice regarding parallel processing.
These are the specifications of my iMac:
3.2GHz , Intel Core i5, No. of processor: 1, Total number of cores: 4, L2
Cache per core: 256kb, L3 Cache: 6MB, Memory: 8GB.
Would
On Tue, Jul 3, 2012 at 5:56 PM, Akio Yamamoto
wrote:
> Yes, as Richard pointed out, I just wanted to know the numbers for input
> to Amdahl's law, if you have already something, to figure out the maximum
> expected speedup using multiple processors/cores.
>
> As for improvements of em_reg, I'll t
thanks Akio
hopefully you will contribute the code back if/when you get it working?
Bruce
On
Wed, 4 Jul 2012, Akio Yamamoto wrote:
> Hi Bruce and Richard,
>
> Yes, as Richard pointed out, I just wanted to know the numbers for input
> to Amdahl's law, if you have already something, to figure out
Hi Bruce and Richard,
Yes, as Richard pointed out, I just wanted to know the numbers for input
to Amdahl's law, if you have already something, to figure out the maximum
expected speedup using multiple processors/cores.
As for improvements of em_reg, I'll try to split each transform as well as
par
On Tue, Jul 3, 2012 at 3:48 PM, Bruce Fischl wrote:
> I think that the theoretical ratio is much bigger than what you would be
> able to achieve in practice. It's hard to compute exactly, but for example
> for em_reg it should be the number of samples (which are processed
> independently), so som
Hi Akio
I think that the theoretical ratio is much bigger than what you would be
able to achieve in practice. It's hard to compute exactly, but for example
for em_reg it should be the number of samples (which are processed
independently), so something on the order of 1000. For ca_reg it should
Freesurfer experts,
I have been working on openmp parallelization of Freesurfer programs.
I'd like to know the ratio of sequential processing parts (which are
essentially impossible to be parallelized) to the total amount of
processing in order to calculate the theoretical limit of performance
im
mri_glmfit-sim can be run in parallel. See the --help. Also, I've run a
big batch of simulations and put the results here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mult-comp-cor.tar.gz
this is for whole hemisphere on fsaverage. If that is what you are
doing, then it should b
Hi FreeSurfer users, is it possible to run FreeSurfer on parallel
processors? We would like to run mri_glmfit-sim in parallel to reduce the
run time. Have you any experience running FreeSurfer in parallel, or would
it be relatively easy to reconfigure?
Any thoughts would be greatly appreciated.
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