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.
Step 1: Choose the input folder that contains the DICOM’s (here ‘bidscointutorial\raw’).
Step 2: Select the
../subject/session/..
order of folders.
Step 3: Create and choose the output folder. All BIDSconvertR files (including the ‘user_settings.R’ file) are saved here.
Step 4: Do not use the “subject-ID” or “pattern to remove” features. You have compliant subject-IDs!
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.
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.