The installation procedure

Installing R and RStudio and downloading sample data:

  • To install the BIDSconvertR on Windows or Linux follow the instructions.

  • Download the BIDScoin example data : Download here. Please be aware that the data has been compressed twice using gunzip (suffix: ‘.gz’) and tar (suffix: ‘.tar’). You need to unpack both. Some programs do this in one step, others need to extract it twice. The data is fine, when you can easily click down the folder structure.

The BIDSconvertR workflow

This procedure should demonstrate how to use the BIDSconvertR. We appreciate the BIDScoin team’s permission to use their sample data. This tutorial only covers the basic steps. You can find a detailed description including visualizations in the “workflow” section.

This workflow covers each stage of the BIDSconvertR workflow:

  • Launch RStudio and use the R console from here on.

  • Execute library("bidsconvertr", quietly = TRUE).

  • Use the convert_to_BIDS()command to launch the tool.

Creation of ‘user_settings.R’ file.

  • Create your own ‘user_settings.R’ file by following the popup messages.

    Sequence mapper

    • Step 1: Choose the input folder that contains the DICOM’s (here ‘bidscointutorial\raw’).

    Sequence mapper

    • Step 2: Select the ../subject/session/.. order of folders.

    Sequence mapper

    • Step 3: Create and choose the output folder. All BIDSconvertR files (including the ‘user_settings.R’ file) are saved here.

    Sequence mapper

    • Step 4: Do not use the “subject-ID” or “pattern to remove” features. You have compliant subject-IDs!

    Sequence mapper

GUI: sequence mapper

  • Use the sequence mapper to rename your files in accordance with BIDS, click “save” and close the window. The workflow should automatically launch the next steps.

Image

Here you find the entries as text for copy & pasting. Alternatively, download the sequence_map.tsv from this link, right-click, save, and replace the file in your BIDS output folder.

sequence

BIDS_type

BIDS_sequence

relevant

t1_mprage_sag_ipat2_1p0iso

anat

T1w

1

AAHead_Scout_32ch-head

anat

smart

0

cmrr_2p4iso_mb8_TR0700

func

task-reward_acq-mp8_echo-1_bold

1

cmrr_2p4iso_mb8_TR0700_SBRef

func

task-reward_acq-mp8_echo-1_sbref

1

cmrr_2p5iso_mb3me3_TR1500_e1

func

task-stop_acq-mp3m3_run-1_bold

1

cmrr_2p5iso_mb3me3_TR1500_e2

func

task-stop_acq-mp3m3_run-2_bold

1

cmrr_2p5iso_mb3me3_TR1500_e3

func

task-stop_acq-mp3m3_run-3_bold

1

cmrr_2p5iso_mb3me3_TR1500_SBRef_e1

func

task-stop_acq-mp3m3_run-1_sbref

1

cmrr_2p5iso_mb3me3_TR1500_SBRef_e2

func

task-stop_acq-mp3m3_run-2_sbref

1

cmrr_2p5iso_mb3me3_TR1500_SBRef_e3

func

task-stop_acq-mp3m3_run-3_sbref

1

field_map_2p4iso_e1

fmap

acq-2p4_magnitude1

1

field_map_2p4iso_e2

fmap

acq-2p4_magnitude2

1

field_map_2p4iso_e2_ph

fmap

acq-2p4_phasediff

1

field_map_2p5iso_e1

fmap

acq-2p5_magnitude1

1

field_map_2p5iso_e2

fmap

acq-2p5_magnitude2

1

field_map_2p5iso_e2_ph

fmap

acq-2p5_phasediff

1

Now the data is automatically saved into BIDS, the BIDS validator is started, and the Shiny BIDS viewer starts.