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fmri

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GuannanZhao
GuannanZhao commented Aug 28, 2019

I try to install brainiak on MacOS Mojave just by

python3 -m pip install -U brainiak

following the instruction on Docs » Installation page.
But at the end I still encounter an error as

ERROR: Could not build wheels for brainiak which use PEP 517 and cannot be installed directly

So what's the problem with me? Did I do something wrong?

Thanks,
Zhao

tedana
handwerkerd
handwerkerd commented Dec 13, 2019

Summary

As part of examining #490, I noticed that utils.unmask was called 400 times through the tedana workflow. 352 of those 400 times were following the logged line:
"INFO:tedana.metrics.kundu_fit:Performing spatial clustering of components" My data has 323 volumes.

Next Steps

  • This section of the code should be examined to see if there is any way to call unmask less often o
arokem
arokem commented Aug 3, 2018

Upon running the canlab_toolbox_setup I get this warning

Warning: Function vecnorm has the same name as a MATLAB builtin. We suggest you rename the function to avoid a
potential name conflict. 
> In path (line 109)
  In addpath (line 96)
  In canlab_clone_github_repository (line 164)
  In canlab_toolbox_setup (line 179) 

Might be worth renaming it to avoid name-space collisi

ejolly
ejolly commented Jul 23, 2019

We should swap our current code where we loop over flattened arrays in Brain_Data.similarity() to scipy.spatial.distance.cdist which is 2 orders of magnitude faster.

For example, correlating a 5,000 x 50,000 Brain with a 11 x 50,000 Brain takes ~2:30 min, but with cdist takes about ~ 12 seconds.

thperret
thperret commented Aug 26, 2016

when running the pyhrf_jde_vem_analysis command with the --no-parallel flag, the script forks X processes (X being the number of available threads on the system) even if it doesn't compute the parcels on parallel.
If I don't include the --no-parallel to the command line, each subprocess forks X processes which lead to X² processes which are totally blocking the processor.
I'm really confused

TheChymera
TheChymera commented Mar 21, 2018

Curently, we are testing if all imports work by including this snippet in all modules' __init__.py.

This is quite annoying, since it loads all imports from a module even only if you are only looking to execute one function, and thus raises (perfectly sensible but command-unrelate

Remi-Gau
Remi-Gau commented Aug 18, 2019

We want the web-app to automatically generate a method section.

We therefore need to have some template or boilerplate method section with empty placeholders to be filled in by the different options chosen by users when they fill the list.

This requires writing those boilerplate texts for each activity of the checklist.

  • This might need identifying which set of items can be grouped tog

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