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March 29, 2022 02:16PM
Hello,

The most comprehensive example of this is AFNI_demos/AFNI_pamenc, which we have presented during the more recent bootcamps as part of the CD/AFNI_demos.tgz package. That contains a complete set of scripts for running FreeSurfer, @SSwarper, afni_proc.py and group analysis (3dttest++, including cases of -ETAC and -ClustSim).

There is a more recent example of processing scripts called APMULTI_Demo1_rest, which can be installed by simply running:
@Install_APMULTI_Demo1_rest
But while demonstrating options for processing multi-echo rest data, it does not contain anything to loop over subjects.

Both of those packages contain scripts for running on one's desktop, or on an HPC system with swarming.

The scripts in APMULTI_Demo1_rest are what we currently base new analyses on, though again, to keep them simple, they do not loop over subjects.
The AFNI_pamenc scripts do loop over subjects, but they are not quite as nice as the APMULTI scripts.

In any case, please take a look and feel free to ask any questions about them.

- rick
Subject Author Posted

shell script for the preprocessing step for all subjects Attachments

osman March 29, 2022 08:02AM

Re: shell script for the preprocessing step for all subjects

rick reynolds March 29, 2022 02:16PM

Re: shell script for the preprocessing step for all subjects Attachments

osman March 29, 2022 04:15PM

Re: shell script for the preprocessing step for all subjects

ptaylor March 29, 2022 04:42PM

Re: shell script for the preprocessing step for all subjects

Philipp April 21, 2022 08:58AM



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