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OASIS-brains download tutorial.

Presentation · September 2019

DOI: 10.13140/RG.2.2.18908.03205

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Ana Maldonado
Tecnológico de Monterrey
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All content following this page was uploaded by Ana Maldonado on 20 September 2018.

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MRI’s database
benchmark
18.09.2019
ALMG
Downloading OASIS-3 (OASIS Brains Datasets)
from Xnat
https://central.xnat.org/app/template/XDATScreen_report_xnat_projectData.vm/search_element/xnat:projectData/s
Step 1: Click on the following link to earch_field/xnat:projectData.ID/search_value/OASIS3
open Xnat

Step 2: Register in Xnat https://central.xnat.org/app/template/Register.vm

Step 3: Request access to all of the https://www.oasis-brains.org/

OASIS-Brains datasets and agree to
all of their terms

Wait a day or two for your approval :)

Downloading OASIS-3 (OASIS Brains Datasets) from
Xnat
Now you can log in! :)
Downloading OASIS-3 (OASIS Brains Datasets) from Xnat
Step 4: Enter Oasis-brains.org, scroll down and https://www.oasis-brains.org/
click under the Get Data subtheme on
“Scripted Download Instructions” (SDS). Click
on the Github link.

https://github.com/NrgXnat/oasis-scripts

Step 4.1: Creating a Spreadsheet CSV from https://central.xnat.org/app/template/XDATScreen_report_xnat_projectData.vm/search_element/x

XNAT Central: nat:projectData/search_field/xnat:projectData.ID/search_value/OASIS3
a.) Click on Browse Oasis Data.
 Downloading OASIS-3 (OASIS Brains Datasets) from Xnat
b.)Click on OASIS3 → “Add Tab” → MR https://central.xnat.org/app/template/XDATScreen_report_xnat_projectData.vm/search_element/xnat:project
Sessions (in our case) → then click on Data/search_field/xnat:projectData.ID/search_value/OASIS3
options → Spreadsheet and download
the CSV file (In Windows it will be
downloaded as an Excel file).
 Downloading OASIS-3 (OASIS Brains Datasets) from Xnat
c.) Delete all
the columns,
but the one
with the MR Before :)
ID’s. Delete
the titles as
well! :)

Midway :)
Save it with
any name you
like :).

In my case it
will be: D.csv
Almost final
document :)
Downloading OASIS-3 (OASIS Brains Datasets) from Xnat

We are going to do this

step later, after installing
and setting MobaXTerm.

*For Windows users.

 Downloading OASIS-3 (OASIS Brains Datasets) from Xnat
Step 4.2: Download the Github Oasis https://github.com/NrgXnat/oasis-scripts
script and Unzip it! :) (I downloaded it to
a folder called “Defying gravity” on my
Desktop).

Folder or directory break! The OASIS github repository includes

the following scripts:
You should save your CSV file (in my
case the D.csv) in the same folder where
the script is.

E.g., both
download_oasis_scans_wget.sh and
D.csv should be in the same folder.

My path is:
C:\Users\admin\Desktop\DefyingGravity\
OASIS\oasis-scripts-master
 Downloading OASIS-3 (OASIS Brains Datasets) from Xnat
Scripts time! https://github.com/NrgXnat/oasis-scripts

download_oasis_scans.sh → works on Linux or

Mac; you should have the zip program installed.

download_oasis_scans_tar.sh → works with

MobaXTerm (Windows if you do not have the zip
program installed on your machine).

download_oasis_scans_wget.sh → Both, Windows

and Linux, in case you start getting the “curl” error.

Step 5: https://mobaxterm.mobatek.net/download.htm
Open a terminal window (on Mac) or Command
line (on PC/Linux)
● For Mac: You can use Terminal.
● For Windows: download the MobaXTerm
terminal system.

MobaXTerm: I downloaded the Portable Home

Edition (MobaXterm Home Edition v10.9), and
saved it and unzipped it in my Downloads Folder.
 Downloading OASIS-3 (OASIS Brains Datasets) from Xnat
5.2 Add your
5.1 Open MobaXterm and click on Settings Persistent home
directory

In my case:
_DesktopDir_\DefyingGr
avity\OASIS\oasis-script
s-master

5.4 Write your commands! :)

5.3 Start your local
terminal 5.4 a.) Formatting your .csv file.
5.4 b.) Downloading the
OASIS-3 scans.
5.4a This step will add the Unix format to your .csv file

● tr -d '\r' < myfile.csv > myfile_unix.csv

● tr -d '\r' <D.csv> D1.csv
*This is the name I wanted to give to the new formatted .csv file. Do not delete the “<>” signs.
5.4b
./download_oasis_scans_wget.sh <input_file.csv> <directory_name> <xnat_central_username> <scan_type>

./download_oasis_scans_wget.sh D1.csv muriel Anafab93 T1w

*I chose the wget script because of the curl error; my input file is the D1.csv; in directory name I wrote the name of the folder I wanted to
create to save the files, in this case “muriel”; Anafab93 is my username + I only wanted to download T1w scans.
A brief review of inputs and scan types
Required inputs: ● https://github.com/NrgXnat/oasis-scripts#downloading-mr-and-pet-scan-files
● https://github.com/NrgXnat/oasis-scripts#download_oasis_scanssh
./download_oasis_scans.sh
<input_file.csv> ● <input_file.csv> - A Unix formatted, comma-separated file containing a column for experiment_id (e.g.
<directory_name> OAS30001_MR_d0129) → D.csv
<xnat_central_username>
<scan_type> ● <directory_name> - A directory path (relative or absolute) to save the scan files to. If this directory doesn't
exist when you run the script, it will be created automatically. → muriel
●
<xnat_central_username> - Your XNAT Central username used for accessing OASIS data on
central.xnat.org (you will be prompted for your password before downloading) → Anafab93

● <scan_type> - (Optional) The scan type of the scan you want to download. (e.g. T1w, angio, bold,
fieldmap, FLAIR) You can also enter multiple scan types separated by a comma with no whitespace (e.g.
T2w,swi,bold). Without this argument, all scans for the given experiment_id will be downloaded. → T1w

https://github.com/NrgXnat/oasis-scripts#list-of-available-scan-type-names
List of available scan type
When entering scan_type into your script, use any of the following names: angio, asl, bold, dwi, fieldmap, FLAIR,
names
GRE, minIP, swi, T1w, T2star, T2w For more information on these scan types, see the OASIS Imaging Data
Dictionary
Main references
GitHub NrgXnat/oasis-scripts. (2018, September 7). NrgXnat/oasis-scripts. Retrieved September 18, 2018, from

https://github.com/NrgXnat/oasis-scripts#list-of-available-scan-type-names

Mobatek. (n.d.). MobaXterm free Xserver and tabbed SSH client for Windows. Retrieved September 18, 2018, from

https://mobaxterm.mobatek.net/

Open Access Series of Imaging Studies. (n.d.). OASIS Brains. Retrieved September 18, 2018, from https://www.oasis-brains.org/

XNAT. (n.d.). CENTRAL. Retrieved September 18, 2018, from

https://central.xnat.org/app/template/XDATScreen_report_xnat_projectData.vm/search_element/xnat:projectData/search_field/xnat:pr

ojectData.ID/search_value/OASIS3
 I hope this little
tutorial may help
you :)
Ana

Further questions: anafab93@gmail.com

Thank you for your help and suggestions: Diego, Angus,

Astrid, Jorge, Gris and Lars.

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