[Freesurfer] OHBM Brainhack 2021

[tibor.auer]

External Email - Use Caution

Dear all,

 

We are happy to announce the upcoming Organization for Human Brain Mapping
(OHBM) Brainhack 2021 happening June 16-18 around the clock around the
world! Join the party by registering here
  ($25
fee, or optional fee waiver; check out some project proposals here

 ).

 

We are also looking for volunteers to help spread the word and facilitate
Brainhack activities. We'd like to recruit around 100 volunteers-so any
contribution is more than welcome, no prerequisites needed! Volunteer by
filling out this form 

  (more
information about volunteer roles here
 ).

 

About Brainhack:

Brainhacks 

  (including OHBM Brainhack

 ) are events promoting
interdisciplinary neuroscience research; they bring researchers together
from a variety of subfields (e.g., neurobiology, psychology, computer
science, etc.) and research backgrounds (e.g., medical student, industry
professional, RA, etc.) to collaborate on projects and ideas and teach open
science-oriented technical skills. The focus on intensive community- and
skill-building opens doors to a number of professional opportunities (learn
more about these benefits here

 ).
Brainhacks are not your typical hackathon-they are actively inclusive rather
than competitive. To that end, even if you have never attended a hackathon
before or written a line of code, you are welcome! No need to work with
neuroimaging methods or be part of OHBM to attend. All you need is to come
along and share your ideas, expertise, contributions with whatever pace and
form you can make it happen while having a chance to collaborate and meet
with many other researchers all around the world!  

 

We particularly welcome the contributions of groups traditionally
underrepresented in neuroscience, including women, BIPOC, LGBTQ+,
individuals with disabilities, and more. Brainhacks are safe spaces, with a
policy of zero tolerance for harassment. OHBM Brainhack 2021 is intended for
everyone to feel safe, learn from each other and share knowledge. Our event
would be enriched by your involvement and contributions. To support our
mission, please share this widely-we'd especially love your help translating
and sharing this message in your local language to reach as many people
around the world as we can! 

Re: [Freesurfer] Running Freesurfer in the Desktop

[tibor.auer]

External Email - Use Caution

Hi Rosie,

 

You need to specify the SUBJECTS_DIR variable to tell FreeSurfer where to 
create the subject’s directory with the processed data.

 

If you use BASH:

export SUBJECTS_DIR=/home/rosalia/Desktop/ARTICO

will result in creation of /home/rosalia/Desktop/ARTICO/sub-003_ses-BSL_T1w.nii

 

BWT, I recommend leaving the “.nii” from the subject name. I.e.:

recon-all -s sub-003_ses-BSL -i 
/home/rosalia/Desktop/ARTICO/sub-003_ses-BSL_T1w.nii -T2 
/home/rosalia/Desktop/ARTICO/sub-003_ses-BSL_T2w.nii -T2pial -all

 

Kind regards,

Tibor 

 

Auer, Tibor M.D. Ph.D.

Research Fellow

School of Psychology, Faculty of Health and Medical Sciences

University of Surrey, Guildford GU2 7XH

  t.a...@surrey.ac.uk

 

 @TiborAuer

 

Feladó: freesurfer-boun...@nmr.mgh.harvard.edu 
 E személy nevében: Rosalia Dacosta 
Aguayo
Küldve: 19 June 2021 12:36
Címzett: Freesurfer support list 
Tárgy: [Freesurfer] Running Freesurfer in the Desktop

 

External Email - Use Caution

Dear Freesurfer's team,

 

I am trying to run FreeSurfer recon-all -all in a folder placed on my Desktop 
and I am having some trouble. 

 

rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ recon-all -subject 
sub-003_ses-BSL_T1w.nii -i /home/rosalia/Desktop/ARTICO/sub-003_ses-BSL_T1w.nii 
-T2 /home/rosalia/Desktop/ARTICO/sub-003_ses-BSL_T2w.nii -T2pial -all
mkdir: cannot create directory 
'/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii': Permission denied
mkdir: cannot create directory 
'/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii': Permission denied
mkdir: cannot create directory 
'/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii': Permission denied
cp: cannot create regular file 
'/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii/scripts/build-stamp.txt':
 No such file or directory
cat: 
/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii/scripts/build-stamp.txt: 
No such file or directory
INFO: FreeSurfer build stamps do not match
Subject Stamp: 
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii/scripts/patchdir.txt: No 
such file or directory.

 

 

I would greatly appreciate your help.

Kind regards,

Rosie

 

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Re: [Freesurfer] RAM per CPU for running Freesurfer 7.1

[tibor.auer]

External Email - Use Caution

Hi Ajay,

 

I also use clusters on a day-to-day basis, and my typical resource requirement 
includes 8GB RAM, which is enough for 80% of my use cases. However, I have not 
processed data with very high resolution (<1mm iso).

 

Regarding core count, you may want to consider the total amount of RAM you can 
put into your nodes. I.e. if you have only 512 GB RM, you can run <64 jobs with 
8GB RAM (some memory is reserved for the system).

 

Kind regards,

Tibor 

 

Auer, Tibor M.D. Ph.D.

Research Fellow

School of Psychology, Faculty of Health and Medical Sciences

University of Surrey, Guildford GU2 7XH

  t.a...@surrey.ac.uk

 

 @TiborAuer

 

Feladó: freesurfer-boun...@nmr.mgh.harvard.edu 
 E személy nevében: Ajay Kurani
Küldve: 12 July 2021 21:39
Címzett: Freesurfer support list 
Tárgy: [Freesurfer] RAM per CPU for running Freesurfer 7.1

 

External Email - Use Caution

Hi Freesurfer Experts,

   I am designing some new hardware for a mini-cluster running Freesurfer and 
other neuroimaging toolboxes and wanted to better understand requirements from 
Freesurfer.

 

1) Is there a minimum amount of ram per core that is needed/recommended or is 
the amount of ram only defined per subject.  Most of the threads I found say 
you need a minimum of 4 GB ram but these were from a long time ago and may not 
apply to the OPENMP code.  Our compute node will have between 52-64 cores so I 
wanted to know what is the ratio for Ram to CPU (multithreading turned off) 
that is recommended as opposed to Ram per subject. 

 

2) AMD vs Intel

We will run jobs on an existing cluster that has Dual Intel Xeon 6230R and for 
our new minicluster we are debating between AMD and Intel.  While AMD offers 
higher core-count per CPU, I am worried that results could potentially differ 
based on the CPU/underlying libraries.  We plan on using docker images so from 
your perspective do you have a recommendation ?

 

Best,

Ajay

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[Freesurfer] Registration, abstracts, & investigator-led abstracts open for INCF Neuroinformatics Assembly 2023!

[tibor.auer]

External Email - Use Caution

Dear FreeSurfers,

 

Apologies for the cross-posting! 

 

Join us for Assembly, hosted once again on the Gather platform! We are
currently looking for speakers for two investigator-led sessions, poster
presenters, and of course Assembly registrants. Our annual Assembly is a
unique venue where neuroscience researchers, tool developers, standards
developers, and infrastructure providers can meet with potential
collaborators and hear about the latest advancements in neuroinformatics and
FAIR neuroscience.

 

 
 Submit an abstract (poster)

 
 Submit an abstract
(investigator-led session)

 

Our program this year stretches from September 19 to September 21, and is
centered around workshops proposed by our community. Sessions comprise
presentations, investigator-led talks, round-table discussions, tutorials,
and hands-on workshops.

 

 
 Register for Assembly

 
 See the program