Parallel computation in the stage of "Prepprocessing with fmriprep".

Submitted by Zeqiang Linli on Tue, 06/15/2021 - 17:01

Dear Dr. Yan

When I used the DpabiSurf to pre-processe the DemoData posted in this website, I noted that the parallel computation in matlab was not work during the stages of “Convert to BIDS” and “Preprocessing with fmriprep”, in other word, 3 subjects was preprocessed  one by one in order, which is very time comsuming. But in the latter stages such as “slice order”, the parallel computation was work. Although that, “Preprocessing with fmriprep” is the most time comsuming stage and we may more need to do parallel computation in this stage.

I noted that when I installed and setted the DpabiSurf and Docker, I can not to Set User/Memory since this setting is not avaiable in the new version of Docker. Does it have anything to do with this.

Some information of my computing platform:

Operation system: Windows Pro 10
Matlab 2018b
DpabiSurf 1.6
Docker 3.33
number of core: 12
RAM: 64G


Thanks for any help given.

Best,

Zeqiang

 

 

 

 

Forums:

YAN Chao-Gan

Fri, 06/18/2021 - 09:01

Hi Zeqiang,

When running fmriprep, MATLAB parallel workers would be closed.

However, it's still running in parallel with fmriprep with the number of workers you defined. Using linux's parallel other than matlab's.