Overview

This program generates a birthday card from an individual's structural MRI. It takes the brain image, identifies an attractive sagittal slice, overlays a party hat image, text that states “Happy Birthday” and “We Lobe You” on this slice, and creates an output image as shown below.

Program requirements

This program is a Bash shell script that uses programs from the FSL software suite. It has been tested in Linux but should also run on macOS.

• Prerequisites. FSL and ImageMagick should be installed.
• Inputs. The program requires the full structural scan and the skullstripped structural scan.

We have tested this program on subjects from multiple studies, ranging in age from approximately 10-90 years. Please let us know of any problems!

Purpose

This program allows us to thank participants for their contribution to research, conveying to them that their time is important and appreciated by using their MRI data to create an inexpensive but unique keepsake.

How to use

Downloading

There are two ways to download this program. Use the first method if you do not have git installed, or are not comfortable with git.

1. As a zip file from Github

   1. Download the zip file from IBIC/birthdaycard
   2. Extract the zip file birthdaycard-master.zip in your home directory
   3. A new directory named birthdaycard-master will be created
   4. You can change into this directory to run the example. We will refer to this directory as birthdaycard in the remainder of this document. You can rename it if you wish.

2. Using Git

Type the following command at your prompt:

git clone https://github.com/IBIC/birthdaycard.git

Now you will have a directory named birthdaycard. You can change into this directory to run the example.

Running the Program

For demonstration purposes we have included two NiFTI files, a structural (T1.nii.gz) and skull stripped version (T1_skullstripped.nii.gz). This is subject 50777 from the publicly available ABIDE data set. We have given this subject the name "Alex Doe".

Note that the program assumes that the orientation of the NiFTI files matches those of the standard MNI template image.

If the T1 image is rotated such that the hat is not aligning properly, apply the T1 to MNI standard space and then use the standardized T1.

Quick Start

To run, cd into the birthdaycard directory and type the following.

./ibic_birthdaycard -t sampledata/T1.nii.gz -s sampledata/T1_skullstripped.nii.gz -o alexdoe -n "Alex Doe"

You see output on the terminal that looks like this.

The file name of the created card will be will be "alexdoe.jpg", and the path will be displayed in the terminal. You can view it by how to view. It should look like the example above.

How to View

The output file path will be printed in the terminal. In the above example, the file has been placed in the birthdaycard directory. This is the default location. To view this file, use an image viewer, such as eog Alexdoe.jpg or use a browser such as firefox Alexdoe.jpg

More Detailed Usage

The program has 5 different flags. Flags -t, -s, -o, and -n are required, and flag -d is optional. The order does not matter. These flags and their descriptors can be found by typing

./ibic_birthdaycard -h

The -t flag specifies the name of the full structural scan file. (Must be in standard orientation)

The -s flag specifies the name of the the skull stripped structural scan file. (Must be in the same space and overlap with the full structural scan file.)

The -o flag specifies the output image file name (a .jpg extention is automatically added)

The -n flag specifies the name displayed in the birthday card (put name in quotations to retain spaces)

The -d flag is optional and used to determine which sagittal slice to use for the card, counted in centimeters, for the best image. By default, a sagittal slice 1mm to the right or left of the midline is selected. Use this flag to override this selection if the sagittal slice selected by default is not attractive.

It is important to verify that the sagittal slice chosen is an attractive full brain that will not scare the participant.

Source

Output

The file name and the path to where it was saved will be shown in the terminal. In this case, it will look like this

~/birthdaycard/alexdoe.jpg

By default this output is a 4x6 image that is viewable in a browser by running a command similar to

firefox ~/birthdaycard/alexdoe.jpg

Installing

After you have downloaded the program as above, you will have a directory called birthdaycard which contains the programs. This directory contains the ibic_birthdaycard shell script, and a lib directory with supporting files (e.g., the image of the birthday hat).

By default, if you cd into the birthdaycard directory and run the ibic_birthdaycard program, everything will work correctly.

However, if you wish, you can install the program for all users. Copy the lib directory into a shared location, and edit the ibic_birthdaycard program to include the new location of your lib directory.

Replace $(pwd)/lib with the desired path.

Alternatively, you can set the environment variable LIB_IBIC_BIRTHDAYCARD in your .bashrc to point to the new path, and this will override anything. You could use this feature, for example, to change the text or the hat images to something else.

Assembling and Distributing the Cards

This process is entirely up to the end user, but we will share what we have found to work best for us.

We print the images at Bartells (using a self print kiosk that can pull files off a USB drive) and insert them into frame card holders. This gives us a system where we can decorate frame card holders in advance for different studies and populations. The frame card holders can be decorated with markers, embossing powder, stamps, etc.

The default image size is 4 inches wide by 6 inches tall, which can be changed in the program. As of this writing, Bartells charges $0.19 cents for each 4x6" print, and Amazon charges $0.09 cents for each print; this size is quite affordable.

The cards and envelopes can be purchased online in bulk and prepared in advance. We also include an insert that makes it clear that the card is made from the participant's own image, thanks the participant for their contribution, and includes contact information for the site. We have included an example of our insert. These can be printed 4 to a page, cut out, and placed in the card.

We have found that it is easiest to assemble and decorate cards at the begining of the year, organize them by birthday month, and mail cards at the end of every month for birthdays occurring in the next month. We have also found that Mail Merge is a good tool for creating mailing labels.

In this way, assembling and decorating the cards can be done all at once, and gives a good excuse to get the entire office together for a fun decorating party.

Here are some sources for frame cards that hold 4x6" photos.

Black Frames

Black Envelopes

White Frames and Envelopes

Credits

This program was a team effort from conception to distribution. These are the people who helped at many steps along the way.

• Christina Caso
• An Wang
• Briana Lee
• Trevor Day
• Ji-Min Park
• Josh Wolfe
• Tara Madhyastha