Downloading Data from Flywheel

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Table of Contents

1. Downloading Data from Flywheel
2. Downloading fMRIPrep Data
3. Downloading Specific Data: The fw download Command
4. Downloading BIDS Files: The fw export bids Command

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Downloading fMRIPrep Data

1. Log into Amarel
2. Make sure your profile is set up to automatically activate the Holmes Lab Conda environment.
   • Go to your terminal, and run:

     $ nano ~/.bashrc
     

   • Add the following lines to your bashrc– this will mean that every time you sign into Amarel, your account will automatically activate the Holmes Lab Conda. Thus, any slurm scripts will also use the Holmes Lab Conda

# Set up for conda
. /projects/community/py-data-science-stack/5.1.0/kp807/etc/profile.d/conda.sh

# Activate conda
source /projects/community/py-machine-learning/intel18/cuda12/pgarias/etc/profi$
conda activate /projects/community/holmesenv

1. In terminal or the Amarel OnDemand GUI ()

Downloading Specific Data: The fw download Command

Sessions, acquisitions, and files can be downloaded individually using the fw download command.

Usage

fw download [-h] [--config-file CONFIG_FILE | --no-config] [-y] 
[--ca-certs CA_CERTS] [--timezone TIMEZONE] [--debug | --quiet][-o [OUTPUT]] [-p PREFIX] [-i INCLUDE] [-e EXCLUDE] <source-path>

Arguments

Argument	Description
source-path	REQUIRED: The location of the file on your Flywheel instance. For example [fw://group/project/subject/acquisition/attachments]
-i FILE_TYPE, --include FILE_TYPE	Download only files with the specified types.*
-e FILE_TYPE, --exclude FILE_TYPE	Ignore files with the specified types.*
-o, --output file name	Name of the folder where the data is downloaded
-p PREFIX, --prefix PREFIX	Prefix for downloaded directory structure

For a full, up-to-date list of options, run the following from your command line:

fw download --help

• Learn more about file types in Flywheel

Example: Downloading Acquisition Files

Below is an example of how to download a particular subject:

Find the files

1. Find which group you need files from. You can return all the “groups” you’re a part of (and your permissions) by running run fw ls. The Holmes Lab “group” in flywheel is 022, so it may say:

$ fw ls Output: rw 022

1. Next, figure out what “project” they’re in. Running fw ls 022 will return all the projects in the Holmes Lab group

   [netID@amarel ~]$ fw ls 022
   rw   Napls       
   rw   PCX         
   rw   ConteCenter 
   

2. See what data is availabe in the project you’re interested in. For example

   [kj537@amarel2 ~]$ fw ls 022/Napls
   rw                          analyses/bids-pre-curate 05/03/2025 17:41:29 
   rw                          analyses/curate-bids 05/03/2025 17:47:15     
   rw     5B May 03 2025 22:47 files/README.txt                             
   rw   200B May 03 2025 22:47 files/dataset_description.json               
   rw  1.1KB May 03 2025 22:47 files/participants.txt                       
   rw                          sub-NDARZN877YYQ                             
   rw                          sub-NDARZP892XY9                             
   rw                          sub-NDARZW884MZC          
   

3. You can investigate the contents of subjects (acquisition files) or specific analyses. For example

[kj537@amarel2 ~]$ fw ls "022/ConteCenter/PCR2Pilot/001/analyses/bids-fmriprep 03/14/2025 11:22:35"
files/bids_tree.html
files/bids-fmriprep_001_67d449d202be158786fab2d3.zip
files/fmriprep_log.txt
files/sub-PCR2Pilot.html.zip

Download the files

To download files, run fw download /path/to/files.

[kj537@amarel2 ~]:~ AvaAnderson$ fw download "022/ConteCenter/PCR2Pilot/001/analyses/bids-fmriprep 03/14/2025 11:22:35"
This download will be about 218 KB comprising 4 files.
Continue? (yes/no): yes
Wrote 218 MB to 2025 11:22:35.tar

Downloading BIDS Files: The fw export bids Command

To download the BIDS versions of files (ie the output of the BIDS Curation gear), you don’t use the fw download on the BIDS Curation analysis. That will just download the acquisitions.tsv and other tsvs which were the outputs of that gear. To download the files in BIDS format, use the fw export bids command.

The formula is: fw export bids -p "<project>" -g "<group>" /path/to/destination/folder

For the Holmes Lab: group = 022 project = ConteCenter, PCX, Napls, …

So a download command may look like:

fw export bids -p "ConteCenter" -g "022" ~/flywheel_download

You can also download specific subjects, using the –subject flag. For example:

fw export bids -p "ConteCenter" --subject PCR2Pilot -g "022" ~/flywheel_download