Introducing myself - Yile Wang

Cyberteams TRECIS
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Hello everyone,

My name is Yile Wang. I am a master student from School of Behavioral and Brain Science. I am working on processing neuroimaging data at Dr. Ana Solodkin’s lab. We are trying to use a computational platform, the virtual brain (TVB) to do individualized large-scale brain modeling and brain dynamics modeling.

Experience on HPC:

In last semester, I learned a little about how to run our program in Ganymede. However, I am still a rookie in this game. I would love to study more about HPC, including how to deploy our platform in HPC and how to submit our jobs to the system.

My workflow:

For data preprocessing, I used pipeline to process raw T1w, T2w or DTI data on linux system. For the data analysis and visualization, I usually use Python and R in my Windows system. All these works are done locally.

Challenge:

One of the biggest challenges for me is that it will cost long time when I am doing preprocessing on every subject’s MRI data. In our ongoing project, we will need to analyze over a hundred people’s neuroimaging data, so I really need help from HPC to accelerate the process.

Thanks~

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Hey @ylwang, welcome :slight_smile:
I am a post-doc at BBS who does preprocessing of neuroimaging data s well (I’m in Gagan Wig’s lab). Do you know what kind of software/tools you guys need for preprocessing?
FSL? SPM? AFNI? FreeSurfer? Do you have a way that you currently link all the steps together (mayeb via Nipype or fmriprep?).

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Hey Micaela @mychan ! Thanks for your message!

Well about the preprocessing tool, I am using a ukbiobank pipeline, which linked all the steps together (including AFNI, FSL, freesurfer). I attached a link below and you can check it for more details.

Hope it helps!

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Cool, thanks. @lhan and I are looking to run the Human Connectome Project pipeline on Europa, we might end up with a lot of similar base software (FSL, FreeSurfer, etc). I will make a post asking to have it install, u can chime in to see if you have additional needs.

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Welcome Yile!

I know initially you were using the TVB web portal for running jobs and trying to learn the python API so you can do more advanced workflows.

Is that where you are? Are you now using straight python or are you still mostly using the web portal or the jupyter interfaces?

From what I recall, most of your workflows (multi patient) are independent. Is that correct? That is, if you’re using python directly and your patient processing pipeline is independent, we can do some simple scripting to scale your workloads horizontally.

I’ll follow up on the software stack in @mychan’s other post.

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Hi Dr. Simmons @csim ~

Sorry for my late response! Yes in fact currently most of my work concentrates on using straight python package of TVB. Also, all of my workflows will be independent so you are right that we can just do some scripting to submit our jobs horizontally to the system!

About the software stack, basically all the dependencies I need are
FSL
AFNI
Freesurfer
Anaconda/Miniconda
git (>=2)
gfortran (installation only)

I will let you know if our lab requires more pre-installed packages~

Thanks so much! Looking forward to more to come!

Yile

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Welcome Yile !

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Hey Yile,

gfortran is part of the default compiler stack for Europa.

[csim@europa ~]$ ml list

Currently Loaded Modules:
  1) autotools   2) prun/2.0   3) gnu9/9.3.0   4) ucx/1.8.0   5) libfabric/1.10.1   6) openmpi4/4.0.4   7) ohpc

 

[csim@europa ~]$ which gfortran
/opt/ohpc/pub/compiler/gcc/9.3.0/bin/gfortran

git is also available

[csim@europa ~]$ which git
/usr/bin/git
[csim@europa ~]$ git --version
git version 2.18.4

Miniconda is available as a module

[csim@europa ~]$ ml load miniconda
[csim@europa ~]$ which conda
/opt/ohpc/pub/unpackaged/apps/miniconda/4.8.3/bin/conda

As is FSL

[csim@europa ~]$ ml show fsl
----------------------------------------------------------------------------------------------------------------------------------------------------
   /opt/ohpc/pub/unpackaged/modulefiles/fsl/6.0.4:
----------------------------------------------------------------------------------------------------------------------------------------------------
whatis("Name: FSL ")
whatis("Version: 6.0 ")
whatis("Category: runtime ")
whatis("Description: analysis and visualization tool for MRI data  ")
whatis("URL https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/ ")
depends_on("openblas")
setenv("FSLDIR","/opt/ohpc/pub/unpackaged/apps/fslbinary/6.0.4")
setenv("FSLOUTPUTTYPE","NIFTI_GZ")
setenv("FSLMULTIFILEQUIT","TRUE")
setenv("FSLTCLSH","/opt/ohpc/pub/unpackaged/apps/fslbinary/6.0.4/bin/fsltclsh")
setenv("FSLWISH","/opt/ohpc/pub/unpackaged/apps/fslbinary/6.0.4/bin/fslwish")
setenv("FSLLOCKDIR","")
setenv("FSLMACHINELIST","")
setenv("FSLREMOTECALL","")
prepend_path("PATH","/opt/ohpc/pub/unpackaged/apps/fslbinary/6.0.4/bin")
prepend_path("LD_LIBRARY_PATH","/opt/ohpc/pub/unpackaged/apps/fslbinary/6.0.4/lib")
help([[Sets up your environment for FSL.

]])

For AFNI and Freesurfer, we will get to those in the next week or so.

Happy computing!

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