Re: [Freesurfer] 6.0.1 automatic download

[Chris Gorgolewski]

External Email - Use Caution

Thanks!

Best,
Chris

PS Apologies for brevity and potential typos. This message was composed on
a phone.

On Wed, Sep 12, 2018, 5:06 PM Hoopes, Andrew 
wrote:

> Hi Chris, that is the same version as before. Sorry, our pubftp disk went
> down a few days ago and we had to restore some things manually (I guess the
> original filename was copied). I renamed the tarball back to
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz
>
>
>
> best,
>
> Andrew
>
>
>
>
>
> *From: * on behalf of Chris
> Gorgolewski 
> *Reply-To: *FS Help 
> *Date: *Wednesday, September 12, 2018 at 11:03 AM
> *To: *FS Help 
> *Subject: *[Freesurfer] 6.0.1 automatic download
>
>
>
> *External Email - Use Caution*
>
> Hi,
>
>
>
> I noticed that
>
>
> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz
>
>
> is no longer available, but instead there is
>
>
> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a.tar.gz
>
>
>
> Is it the same thing or an updated version (if so why not 6.0.2)? Is this
> the right way to grab the same 6.0.1 version in a programmatic way?
>
>
> Best,
>
> Chris
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] 6.0.1 automatic download

[Chris Gorgolewski]

External Email - Use Caution

Hi,

I noticed that
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz

is no longer available, but instead there is
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a.tar.gz

Is it the same thing or an updated version (if so why not 6.0.2)? Is this
the right way to grab the same 6.0.1 version in a programmatic way?

Best,
Chris
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Learning which data derivatives matter most

[Chris Gorgolewski]

External Email - Use Caution

Dear all,

To learn which neuroimaging data derivatives (intermediate or final
analysis outputs) matter most to people conducting analyses and reusing
data we have put together a survey: https://goo.gl/forms/5ghpVbiiPHd8BN153

Please take a moment and fill it and most importantly share it with your
colleagues - this feedback is extremely helpful and will help to focus BIDS
Derivatives

standardization work.

I know the survey is not exhaustive (for example does not include very
important modalities such as EEG, MEG, iEEG or PET). I hope we will be able
to perform followup surveys in the near future to fill in those gaps.

Best,
Chris
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

[Chris Gorgolewski]

This looks like a memory issue to me as indicated bu those two lines:

/opt/freesurfer/bin/reconbatchjobs: line 81:  4014 Killed
exec $JOB >> $LOG 2>&1
/opt/freesurfer/bin/reconbatchjobs: line 81:  4017 Killed
exec $JOB >> $LOG 2>&1

You can adjust how much memory of your host machine will be accessible to
your docker containers. More details here:
https://docs.docker.com/docker-for-mac/#memory

Best,
Chris

On Sun, Feb 4, 2018 at 9:29 AM, Dianne Patterson 
wrote:

> Dear All,
> Pardon my ignorance.  I am trying freesurfer for the first time, using the
> BIDS docker container and the standard dataset ds005.
> Although I have specified 2 participants to run, freesurfer exits with
> errors after the first (and does the same if I run the 2nd subject
> separately).
> I am attaching the 3 logs which I take to be most relevant.  I'd be happy
> to provide other logs if they would be useful for understanding the
> problem.
> Any insight into why this is happening would be much appreciated.
>
> Thanks,
>
> Dianne
>
> On Sun, Feb 4, 2018 at 8:43 AM, Chris Gorgolewski <
> krzysztof.gorgolew...@gmail.com> wrote:
>
>> This is not expected.
>>
>> You would need to provide more details (recon-all.log) for anyone to be
>> able to help you. It might be also worth googling the specific error
>> message before hand - it could be that someone else run into this before.
>>
>> Best,
>> Chris
>>
>> On Sat, Feb 3, 2018 at 7:55 PM, Dianne Patterson 
>> wrote:
>>
>>> Since I'm following the example on the github page, using the ds005
>>> dataset, now with the correct license binding, I am surprised to see
>>> freesurfer exiting with errors (but I don't know much about freesurfer):
>>>
>>> I run this:
>>>
>>> docker run -ti --rm -v /Volumes/Main/Working/BIDS_TES
>>> TING/license.txt:/license.txt:ro -v 
>>> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro
>>> -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
>>> /bids_dataset /outputs participant --participant_label 01 02 --license_file
>>> /license.txt
>>>
>>> A few hours later: recon-all -s sub-01 exited with ERRORS at Sun Feb  4
>>> 03:27:11 UTC 2018
>>> And then sub-02 does not run
>>>
>>> Is this what I should expect?
>>>
>>> Thanks,
>>>
>>> Dianne
>>>
>>>
>
>
> --
> Dianne Patterson, Ph.D.
> Research Scientist
> d...@email.arizona.edu 
> or
> dianne...@gmail.com
> University of Arizona
> Speech and Hearing Science 314
> 1131 E 2nd Street, Building #71
> <https://maps.google.com/?q=1131+E+2nd+Street,+Building+%2371&entry=gmail&source=g>
> (Just East of Harvill)
> ==
> If you don't hear back from me (and you expected to),
> I blame the University's new SPAM filter.
> Please write to my gmail account.
> ==
> Antipiphany: That moment when you realize how little you actually know
> ==
>
> --
> You received this message because you are subscribed to the Google Groups
> "bids-discussion" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to bids-discussion+unsubscr...@googlegroups.com.
> To post to this group, send email to bids-discuss...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/ms
> gid/bids-discussion/CAGpV9FLRhSNGsnkv%2BcJHYU_NO3rFc7iPuvf9L
> 0iEgFiUQQdqvw%40mail.gmail.com
> <https://groups.google.com/d/msgid/bids-discussion/CAGpV9FLRhSNGsnkv%2BcJHYU_NO3rFc7iPuvf9L0iEgFiUQQdqvw%40mail.gmail.com?utm_medium=email&utm_source=footer>
> .
>
> For more options, visit https://groups.google.com/d/optout.
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

[Chris Gorgolewski]

This is not expected.

You would need to provide more details (recon-all.log) for anyone to be
able to help you. It might be also worth googling the specific error
message before hand - it could be that someone else run into this before.

Best,
Chris

On Sat, Feb 3, 2018 at 7:55 PM, Dianne Patterson 
wrote:

> Since I'm following the example on the github page, using the ds005
> dataset, now with the correct license binding, I am surprised to see
> freesurfer exiting with errors (but I don't know much about freesurfer):
>
> I run this:
>
> docker run -ti --rm -v /Volumes/Main/Working/BIDS_
> TESTING/license.txt:/license.txt:ro -v 
> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro
> -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
> /bids_dataset /outputs participant --participant_label 01 02 --license_file
> /license.txt
>
> A few hours later: recon-all -s sub-01 exited with ERRORS at Sun Feb  4
> 03:27:11 UTC 2018
> And then sub-02 does not run
>
> Is this what I should expect?
>
> Thanks,
>
> Dianne
>
> On Mon, Jan 22, 2018 at 9:54 PM, Dianne Patterson 
> wrote:
>
>> Wonderful...and makes total sense!  Thankyou...it is off and running now.
>> -Dianne
>>
>>
>> On Mon, Jan 22, 2018 at 8:19 PM, Chris Gorgolewski <
>> krzysztof.gorgolew...@gmail.com> wrote:
>>
>>> Hi Dianne,
>>>
>>> You need to "mount" the using -v the same way input and output
>>> directories are mounted. For example:
>>>
>>> docker run -ti --rm -v /Volumes/Main/Working/BIDS_
>>> TESTING/license.txt:/license.txt:ro -v 
>>> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro
>>> -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
>>> /bids_dataset /outputs participant --license_file /license.txt
>>>
>>> Best,
>>> Chris
>>>
>>> On Mon, Jan 22, 2018 at 7:13 PM, Dianne Patterson >> > wrote:
>>>
>>>> Dear All,
>>>>
>>>> After trying the example bids app (which worked fine), I am trying the
>>>> freesurfer bids app. I have built the docker container on my mac and I have
>>>> the ds005 data directory here and the license.txt which I requested from
>>>> freesurfer.
>>>> I asked for a linux license (assuming the container contains linux and
>>>> that was the relevant fact).
>>>>
>>>> dpat@Saci:/Volumes/Main/Working/BIDS_TESTING% docker run -ti --rm -v
>>>> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro -v
>>>> /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
>>>> /bids_dataset /outputs participant --license_file "license.txt"
>>>> 1: You should define 'SliceTiming' for this file. If you don't provide
>>>> this information slice time correction will not be possible. (code: 13 -
>>>> SLICE_TIMING_NOT_DEFINED)
>>>> /sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.nii.gz
>>>> /sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.nii.gz
>>>> /sub-01/func/sub-01_task-mixedgamblestask_run-03_bold.nii.gz
>>>> /sub-02/func/sub-02_task-mixedgamblestask_run-01_bold.nii.gz
>>>> /sub-02/func/sub-02_task-mixedgamblestask_run-02_bold.nii.gz
>>>> /sub-02/func/sub-02_task-mixedgamblestask_run-03_bold.nii.gz
>>>> /sub-03/func/sub-03_task-mixedgamblestask_run-01_bold.nii.gz
>>>> /sub-03/func/sub-03_task-mixedgamblestask_run-02_bold.nii.gz
>>>> /sub-03/func/sub-03_task-mixedgamblestask_run-03_bold.nii.gz
>>>> /sub-04/func/sub-04_task-mixedgamblestask_run-01_bold.nii.gz
>>>> ... and 38 more files having this issue (Use --verbose to see them all).
>>>>
>>>> Summary: Available Tasks:  Available
>>>> Modalities:
>>>> 133 Files, 1.77GBmixed-gambles taskT1w
>>>> 16 - Subjects  inplaneT2
>>>> 1 - Sessionbold
>>>>
>>>>
>>>> Traceback (most recent call last):
>>>>   File "/run.py", line 165, in 
>>>> raise Exception("Provided license file does not exist")
>>>> *Exception: Provided license file does not exist*
>>>> ===
>>>> If I provide the full path to the license file, it still fails:
>>>>
>>>> docker run -ti --rm -v 
>>>> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

[Chris Gorgolewski]

Hi Dianne,

You need to "mount" the using -v the same way input and output directories
are mounted. For example:

docker run -ti --rm -v /Volumes/Main/Working/BIDS_
TESTING/license.txt:/license.txt:ro -v
/Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro
-v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
/bids_dataset /outputs participant --license_file /license.txt

Best,
Chris

On Mon, Jan 22, 2018 at 7:13 PM, Dianne Patterson 
wrote:

> Dear All,
>
> After trying the example bids app (which worked fine), I am trying the
> freesurfer bids app. I have built the docker container on my mac and I have
> the ds005 data directory here and the license.txt which I requested from
> freesurfer.
> I asked for a linux license (assuming the container contains linux and
> that was the relevant fact).
>
> dpat@Saci:/Volumes/Main/Working/BIDS_TESTING% docker run -ti --rm -v
> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro -v
> /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
> /bids_dataset /outputs participant --license_file "license.txt"
> 1: You should define 'SliceTiming' for this file. If you don't provide
> this information slice time correction will not be possible. (code: 13 -
> SLICE_TIMING_NOT_DEFINED)
> /sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.nii.gz
> /sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.nii.gz
> /sub-01/func/sub-01_task-mixedgamblestask_run-03_bold.nii.gz
> /sub-02/func/sub-02_task-mixedgamblestask_run-01_bold.nii.gz
> /sub-02/func/sub-02_task-mixedgamblestask_run-02_bold.nii.gz
> /sub-02/func/sub-02_task-mixedgamblestask_run-03_bold.nii.gz
> /sub-03/func/sub-03_task-mixedgamblestask_run-01_bold.nii.gz
> /sub-03/func/sub-03_task-mixedgamblestask_run-02_bold.nii.gz
> /sub-03/func/sub-03_task-mixedgamblestask_run-03_bold.nii.gz
> /sub-04/func/sub-04_task-mixedgamblestask_run-01_bold.nii.gz
> ... and 38 more files having this issue (Use --verbose to see them all).
>
> Summary: Available Tasks:  Available
> Modalities:
> 133 Files, 1.77GBmixed-gambles taskT1w
> 16 - Subjects  inplaneT2
> 1 - Sessionbold
>
>
> Traceback (most recent call last):
>   File "/run.py", line 165, in 
> raise Exception("Provided license file does not exist")
> *Exception: Provided license file does not exist*
> ===
> If I provide the full path to the license file, it still fails:
>
> docker run -ti --rm -v 
> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro
> -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
> /bids_dataset /outputs participant --license_file
> "/Volumes/Main/Working/BIDS_TESTING/license.txt"
>
> Suggestions?  How do I tell freesurfer where the license file is?
>
> Thanks so much,
>
> Dianne
>
>
>
> --
> Dianne Patterson, Ph.D.
> Research Scientist
> d...@email.arizona.edu 
> or
> dianne...@gmail.com
> University of Arizona
> Speech and Hearing Science 314
> 1131 E 2nd Street, Building #71
> 
> (Just East of Harvill)
> ==
> If you don't hear back from me (and you expected to),
> I blame the University's new SPAM filter.
> Please write to my gmail account.
> ==
> Antipiphany: That moment when you realize how little you actually know
> ==
>
> --
> You received this message because you are subscribed to the Google Groups
> "bids-discussion" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to bids-discussion+unsubscr...@googlegroups.com.
> To post to this group, send email to bids-discuss...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/
> msgid/bids-discussion/CAGpV9FJdPWuk7Xw5yAYp-O6iV%
> 3DDiZEcZfDkU8Nzjnn41pEiwcA%40mail.gmail.com
> 
> .
> For more options, visit https://groups.google.com/d/optout.
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Postdoctoral position available in the Poldrack Lab

[Chris Gorgolewski]

Apologies for cross-posting.


The Poldracklab at Stanford is looking to hire a postdoc with expertise in
fMRI data analysis, starting as soon as possible. Our lab is a dynamic and
collaborative group that includes basic cognitive neuroscience researchers
focused on the study of decision making and executive function alongside
methodological researchers focused on reproducible data analysis and data
sharing.  Stanford University is located in sunny northern California, deep
in the heart of Silicon Valley and a short train ride to San Francisco.

The postdoc will be able to contribute to a number of ongoing research
projects in our lab and collaborating labs by analyzing fMRI data from
those studies. In addition, the postdoc will have the opportunity to
develop their own research program with the domain of scientific or
methodological problems currently being investigated within the lab (
https://poldracklab.stanford.edu/projects).

The successful candidate should:

   -

   Have a PhD in a relevant field of study and demonstrated experience with
   the processing and statistical analysis of fMRI data.
   -

   Have strong and demonstrated computer programming skills, including
   Python.  Experience with Nipype is strongly preferred.  Candidates will be
   asked to submit a link to their open source code repository for review.
   -

   Have strong skills in statistics and machine learning.
   -

   Have solid experience with computational data analysis, including strong
   UNIX/Linux skills and experience using high performance computing clusters.
   Experience with cloud computing platforms is also preferred.
   -

   Be dedicated to open source software development and data sharing.

The Poldracklab is strongly committed to diversity in science, and we
particularly welcome applications from members of traditionally
underrepresented groups.

Eligible candidates will be asked to complete a data analysis problem using
a specified dataset and present a report of their results as well as
sharing their analysis code, in order to demonstrate their expertise with
data analysis.

Interested candidates should email the following to russp...@stanford.edu:

   -

   A cover letter describing your background and research interests
   -

   CV (including a link to code repository, e.g. Github, Bitbucket)
   -

   Names and email addresses of two references
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] [job] Program Manager for the Brain Imaging Data Structure project

[Chris Gorgolewski]

Do you have great people skills and enjoy organizing events? Are you
interested in helping neuroscientists exchange data in a more useful way?
The Brain Imaging Data Structure project is looking for a full time Program
Manager - this might be a perfect job for you!

No neuroimaging experience is required, but some will come handy. This
position might be especially attractive if you appreciate working in an
academic environment, but prefer to avoid the stress of “publish or perish”
and enjoy a competitive salary.

The position is based in the legendarily sunny San Francisco Bay Area. The
successful candidate will receive relocation support.

More details at
https://stanford.taleo.net/careersection/2/jobdetail.ftl?job=76713&lang=en#.WeUP-AdO9j4.email.
We will start reviewing applications on the 6th of November.

Best regards,
Chris Gorgolewski

PS Apologies for cross posting - please forward this ad if you know someone
who might be interested.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] FreeSurfer is now available on OpenNeuro.org

[Chris Gorgolewski]

Dear all,

FreeSurfer BIDS App is now available on the OpenNeuro.org platform. This
means that you can run recon-all on your datasets (with longitudinal
pipeline and study specific template estimation) in the cloud for free (see
example results here

).

You can learn more about OpenNeuro.org in the FAQ
 and about the details of the FreeSurfer BIDS
App here .

Let us know if you have any questions!

Best,
The OpenNeuro Team

PS If you are developing a neuroimaging pipeline and would like to host it
on OpenNeuro.org please get in touch. We a non-profit project dedicated to
enabling access to cutting edge neuroimaging methods and incentivizing data
sharing.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Setting -openmp flag to more than 8

[Chris Gorgolewski]

Thank you - this is very useful!

On Tue, May 2, 2017 at 12:05 PM, Bruce Fischl 
wrote:

> Hi Chris
>
> we have found an almost linear speed improvement up to 4, then it starts
> to fall off, with not much at all after 8.
>
> cheers
> Bruce
>
> On Tue, 2 May 2017, Chris Gorgolewski wrote:
>
> Hi,
>> We are running freesurfer as part of a bigger pipelines with other steps
>> that can be performed in parallel to freesurfer reconstruction. So far we
>> have set the openmp flag to the number of all available cores. However,
>> our
>> experience with ANTs and AFNI which also capitalize on the OpenMP
>> parallelization is that there is little benefit of using more than 8-10
>> cores (even if more are available). Does this also apply to FreeSurfer?
>> Does
>> anyone have done some benchmarking of this?
>>
>> Thanks in advance for your help.
>>
>> Best,
>> Chris
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Setting -openmp flag to more than 8

[Chris Gorgolewski]

Hi,

We are running freesurfer as part of a bigger pipelines with other steps
that can be performed in parallel to freesurfer reconstruction. So far we
have set the openmp flag to the number of all available cores. However, our
experience with ANTs and AFNI which also capitalize on the OpenMP
parallelization is that there is little benefit of using more than 8-10
cores (even if more are available). Does this also apply to FreeSurfer?
Does anyone have done some benchmarking of this?

Thanks in advance for your help.

Best,
Chris
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.