[Freesurfer] OHBM Brainhack registration is open!

[Remi Gau]

  External Email - Use Caution
Hey all,



  The OHBM Open Science Special Interest Group (OS-SIG) is very happy to announce:
  
  
Registration is now open for the 2020 OHBM Brainhack (the hackathon organized by the OS-SIG) that will be held online, June 16-18. Register here!
  
  
  
We are providing 50 mini-grants worth 100 USD each to help hackathon attendees set up for online conferencing. Apply via the link above.
  
  
  
  Who is the OHBM Brainhack for?
  
  Watch our short video!


  
  Is my time zone included in the program of the 2020 OHBM hackathon?
  
  Wherever you are in the world, the OHBM Brainhack will happen at a time that is within reasonable working hours. For the first time, the OHBM Brainhack will be a global online event organized around 3 hubs: ‘Asia and Pacific’, ‘Europe, Middle East and Africa’ and ‘The Americas’. Each hub will run at a different time, with a common program shared across the 3 hubs.
  
  
  We thank Openneuro, INCF, CNeuroMod, The Ludmer and CONP, for their generous contributions in support of the OS-SIG.
  
  
  For updates, please visit the OHBM Brainhack website, the OS-SIG website, follow @OHBMopen on Twitter or follow OHBM wechat official account. If you have any questions, please reach out to us at ossig2...@inria.fr.
  
  Kind regards,


  
  Camille Maumet, Liza Levitis and Rémi Gau, on behalf of the Open Science SIG


  
  

  

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[Freesurfer] OHBM Brainhack 2020

[Remi gau]

External Email - Use Caution

Hello all, The OHBM Open Science Special Interest 
Group<https://ossig.netlify.com/> is very happy to announce that the 8th Annual 
OHBM Brainhack will be held  June 23-25 at Phi Centre in Montreal.


A hackathon? For who?

At the OHBM Brainhack, members of the community gather to work collaboratively 
on common projects. This year we would like to especially welcome new attendees 
who have never been to hackathon before. We will provide TrainTrack sessions 
tailored for beginners and opportunities to directly apply new skills by 
joining a hackathon project. All members of the community are invited to take 
part in the OHBM Brainhack 2020!


Applications are now open for the OHBM Hackathon Travel Awards.

The Open Science Special Interest Group is pleased to offer 20 travel awards 
that will include free registration at the hackathon plus $500 USD that will go 
towards covering part of the expenses incurred to attend the hackathon. Submit 
your application no later than March 15th: http://ossig.netlify.com/awards.


Registration for the OHBM Brainhack will open in the middle of March.

Soon after OHBM abstract acceptances are sent out, registration for the OHBM 
Brainhack will open. In the past two years the hackathon was fully booked, and 
we therefore recommend to register early. Seats will be allocated on a first 
come first serve basis. In an effort to increase diversity at the event, we 
will reserve part of the seats to attendees who attend a hackathon for the 
first time or who come from traditionally under-represented groups in science 
or in past hackathons.


Please contribute your favorite TrainTrack session!

Are there specific topics that you would like to see covered in the Hackathon 
training sessions? Please let us know using this 
form<https://forms.gle/LbngA8xVDYj3Ep9W7>.


We are very excited to welcome you to the OHBM Hackathon!

For most recent updates please see the OS SIG 
website<http://ossig.netlify.com/>, follow us on twitter 
@OHBMopen<https://twitter.com/ohbmopen> and follow the hbm-hackathon channel on 
the brainhack 
mattermost<https://mattermost.brainhack.org/signup_user_complete/?id=orpd9qqjb7gqpnwg5k1fdagrq>.

Remi Gau, Elizabeth Levitis and Camille Maumet for the OHBM Open Science 
Special Interest Group
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[Freesurfer] neuroimaging pre-registration template

[Remi gau]

External Email - Use Caution

Dear neuroimagers,

We are organizing a 
hackathon<https://docs.google.com/document/d/1fckBKZEv_Jh0hJ6oVdYuK21krhZtnH0uhwcHp0j0TbE/edit>
 to develop a tool to help researchers creating a pre-registration / 
registered-report for neuroimaging experiments.

The hackathon is embedded in the upcoming meeting of the Society for Improving 
Psychological Science<https://www.improvingpsych.org/SIPS2019/> in Rotterdam, 
NL, July 7-9.

We are thus interested in the challenges that people face when preregistering 
their studies. If you have pre-registered (or currently are pre-registering) 
one of your neuroimaging study, please take 5 minutes to fill in this 
survey<https://docs.google.com/forms/d/e/1FAIpQLSe9IAMFThhpPday_tHvkh1dTGCqjcdKpeb1IspuTMvU48eCPw/viewform>
 and give us any feedback you can.

Thank you for your time!

Johannes Algermissen, David Mehler, Remi Gau, Stephan Heunis
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[Freesurfer] neuroimaging quality control survey

[Remi gau]

External Email - Use Caution

Hello all,

Forward this here as it seems relevant to this mailing list. Do not hesitate to 
circulate this on your institute mailing lists, and ask your collaborators and 
friends.

Thanks

Remi

The neuroimaging quality control (niQC) special interest group (SIG) aims to 
standardize and develop best practices for niQC and Quality Assurance (QA). 
Learn more here: tinyurl.com/WeNeedNiQC


We invite you to fill this survey, to help us to get a sense of various types 
of QC/QA that is done in the neuroimaging community. We would like you to cover 
the "full life-cycle" of neuroimaging research, including but not limited to 
data collection, preprocessing, intermediate outputs and final results. We 
request you to provide details into the various QC/QA processes you conduct in 
your projects. We plan to analyze all the responses from the community to 
identify the challenges our community is facing, consolidate and review 
existing research, develop protocols, compile manuals, improve tools, and make 
recommendations for best practices.


Fill the survey: https://tinyurl.com/niQC-HighLevel-Survey-2019


Find out more about joining this effort to standardize neuroimaging QC here: 
https://groups.google.com/d/forum/niqc


This survey is fully anonymous and we do not track anything. We plan to 
publicly release your input, in its raw form as well as in various forms of 
aggregate summaries. In addition to the aforementioned uses, your response will 
be used for anything else the group would consider necessary in the future to 
advance its mission. Your participation is voluntary and you can withdraw from 
this survey anytime.

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Re: [Freesurfer] use of high res T1 for subcortical segmentation

[Remi Gau]

  
  

  Hey,

Someone corrects me if I am wrong, but it seems that the number of vertices currently allowed with freesurfer cannot accomodate more than a certain number of vertices.
I suspect that the new version of Freesurfer should allow for more vertices.

On high res you might get such error message:
mri_tessellate: max vertices 100 exceeded
recon-all -s Subject_12 exited with ERRORS at Thu Apr 10 11:16:42 BST 2014

Seems the issue has been raised before in this thread: 
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31331.html

Zeke sent me a file of the new mri_tessellate: I can forward it to you if you want.

Best

  Remi Gau
  

  On 10/12/14 10:24, lukas.sch...@ukb.uni-bonn.de wrote:


  Dear Remi!

Thanks a lot for the fast
  response. Could comment further on your point that I might
  need a different version of mri_tesselate ...
The spatial resolution I am
  talking about is 0.5x0.5x0.8 mm3.

Best wihes,

Luke

> Yup.
> 
  > http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon
> 
  > Depending how far you intend to push it, you might need a
  different 
  > version of the mri_tesselate function.
> 
  > Best
        > 
  > Remi Gau
> 
  > On 10/12/14 08:44, lukas.sch...@ukb.uni-bonn.de wrote:
> Hi folks!
> 
  > Is there any way to convince FS to make use of a high
  spatial 
  > resolution (better than 1 x 1 x 1 mm3) for subcortical
  segmentation?
> 
  > Best wishes,

  
  
  
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Re: [Freesurfer] use of high res T1 for subcortical segmentation

[Remi Gau]

  
  
Yup.
  
  http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon
  
  Depending how far you intend to push it, you might need a
  different version of the mri_tesselate function.
  
  Best
  
  Remi Gau
  

  On 10/12/14 08:44, lukas.sch...@ukb.uni-bonn.de wrote:


  Hi folks!

Is there any way to convince FS
  to make use of a high spatial resolution (better than 1 x 1 x
  1 mm3) for subcortical segmentation?

Best wishes,

Luke

  
  
  
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[Freesurfer] 1 PostDoc + 2 PhD positions in Computational Cognitive NeuroImaging; University of Birmingham, UK

[Remi Gau]

*2 PhD and 1 PostDoc positions in Computational Cognitive Neuroimaging; 
University of Birmingham, UK*


In our natural dynamic environment the senses are constantly bombarded 
with many different signals. How does the human brain integrate 
information from multiple senses during perception? To study the neural 
mechanisms of multisensory integration and learning, we combine 
psychophysics, functional imaging (fMRI, EEG/MEG & interleaved TMS-fMRI) 
and models of Bayesian Inference and learning.
The Computational Cognitive Neuroimaging Group (Prof Uta Noppeney) is 
seeking 1 enthusiastic PostDoc and 2 PhD candidates. Applicants should 
have astrong quantitative background and a degree in neuroscience, 
psychology, computer science, physics, medicine or related areas. Prior 
experience in functional imaging, MatLab, data analysis and/or machine 
learning would be an advantage.
The lab is part of the Computational Neuroscience and Cognitive Robotics 
Centre and the Department of Psychology of the University of Birmingham, 
UK. The centre provides an excellent multidisciplinary and collaborative 
research environment combining expertise in cognitive neuroimaging, 
psychophysics and computational neuroscience. The psychology department 
was rated 3rd in the UK research assessment exercise.


Applications will be considered until the positions are filled. Starting 
dates are flexible. For further information, please contact 
u.noppe...@bham.ac.uk  and see
http://www.birmingham.ac.uk/research/activity/cncr/index.aspx 

http://www.birmingham.ac.uk/schools/psychology/index.aspx 


http://www.birmingham.ac.uk/schools/psychology/people/profile.aspx?ReferenceId=29516

For application to the PostDoc positions, please send applications to
http://www.jobs.ac.uk/job/AIM528/research-fellow/
For application to the PhD positions, please send application including 
CV, statement of research interests, and the names and full contact 
details of two referees to:u.noppe...@bham.ac.uk 







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Re: [Freesurfer] basic high res data question

[Remi Gau]

When running this :
recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT_HighRes

mentionned on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon

I get these :

mri_tessellate: max vertices 100 exceeded
recon-all -s Subject_12 exited with ERRORS at Thu Apr 10 11:16:42 BST 2014

Seems the issue has been raised before in this thread: 
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31331.html

So I have a similar request: would it be possible to provide another 
compiled version of mri_tessellate (centos6_x86_64-stable-pub-5.3.0) 
with the an increased max number of faces and vertices?

Sorry to be so needy.

Thanks in advance

Remi Gau


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Re: [Freesurfer] basic high res data question

[Remi Gau]

Hello all,

I have a related question as I am also a freesurfer beginner and 
starting to use it on submilliter MP2RAGE 7T images.


After having had a quick look at the videos, tutos and the archives, I 
found this: http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon

BTW on that page I guess that the line:
"recon-all -mprage -normalization -skulstrip -s $SUBJ"
should read
"recon-all -mprage -normalization *-skullstrip* -s $SUBJ"

For a test run and to familiarize mysef with freesurfer and the trouble 
shooting steps, I ran the "basic" recon-all on one of the native images 
which gave me results at a 1 mm res.


My question is: is there any reason why these steps should work 
differently for a MP2RAGE compared to the MPRAGE described the 
HiResRecon page?


For testing, I am currently running the steps in the page mentioned 
above on one image for practice before running more subjects.


So far, so good but the following command:
mri_nu_correct.mni --i $SUBJECTS_DIR/$SUBJ/mri/orig.mgz --o 
$SUBJECTS_DIR/$SUBJ/mri/nu.mgz --proto-iters 1000 --distance 15 --fwhm 
0.15 --n 1 --uchar $SUBJECTS_DIR/$SUBJ/mri/transforms/talairach.xfm


issued the following warning:
"Use of ?PATTERN? without explicit operator is deprecated at 
~/Program/freesurfer/mni/bin/sharpen_volume line 153."


Thanks

*Remi Gau

*
On 09/04/14 21:57, Torrisi, Sam (NIH/NIMH) [F] wrote:

Good afternoon gurus-

I’m new to FS and working with 0.7mm iso 7T MPRAGEs. After bias-correction with 
AFNI’s 3dUnifize, recon-all ran without hitch but downsampled everything to 
1mm. Now I have basically the same sentiment and question as this thread from 
~2 years ago (i’m linking to the middle for simplicity):

http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg22852.html

What’s the very latest on this? Thanks!

-Salvatore (Sam) Torrisi

Section on the Neurobiology of Fear and Anxiety
National Institute of Mental Health

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