Bids-filter-file as input in a BIDS app

Daniele_Marinazzo · May 24, 2021, 12:54pm

Hi, for our rsHRF BIDS app we are looking for a way to specify some input arguments to filter the datasets to be post-processed (for example if we have different space outputs from fMRIPREP (T1w, MNI, etc) being able to select only a subset for further analysis.

We were then wondering if the bids-filter-file can be customized and used as an input file for rsHRF (or any other BIDS app fwiw), in order to select some specific files for further analyses (i.e. to extend the task label, without too much hard coding)?

Has anyone tried this already?

thanks!

Remi-Gau · May 31, 2021, 7:05am

Hey @Daniele_Marinazzo

If I have understood correctly what you ask, I think you should be able to use pass to get the entities you want to filter. And that includes regular expressions.

Made a quick example notebook, not sure it answers your question.

github.com

Remi-Gau/BIDS-examples/blob/tmp_examples/pybids_query.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Uses [pybids](https://github.com/bids-standard/pybids) on example fmriprep from [bids-example](https://github.com/bids-standard/bids-examples)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from bids import BIDSLayout\n",
    "import os"
   ]
  },
  {

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