Getting started

You can use HippMapp3r through the graphical user interface (GUI) or command line:

For GUI

To start the GUI, type

hippmapper

A GUI that looks like the image below should appear. You can hover any of buttons in the GUI to see a brief description of the command.

_images/hippmapper_gui.png

You can get the command usage info by click the “Help” box on any of the pop-up windows.

_images/hippmapper_help.png

For Command Line

You can see all the hippmapper commands by typing either of the following lines:

hippmapper -h
hippmapper --help

Once you know the command you want to know from the list, you can see more information about the command. For example, to learn more about seg_hfb:

hippmapper seg_hipp -h
hippmapper seg_hipp --help

Hippocampal volumes

To extract hippocampal volumes use the GUI (Stats/Hippocampal Volumes) or command line:

hippmapper stats_hp -h

QC

QC files are automatically generated in a sub-folder within the subject folder. They are .png images that show a series of slices in the brain to help you quickly evaluate if your command worked successfully, especially if you have run multiple subjects. They can also be created through the GUI or command line:

hippmapper seg_qc -h

The QC image should look like this:

_images/hipp_qc_corr.png

Logs

Log files are automatically generated in a sub-folder within the subject folder. They are .txt files that contain information regarding the command and can be useful if something did not work successfully.

File conversion

Convert Analyze to Nifti (or vice versa)

hippmapper filetype

Required arguments:
-i , --in_img    input image, ex:MM.img
-o , --out_img   output image, ex:MM.nii

Example:
hippmapper filetype --in_img subject_T1.img --out_img subject_T1.nii.gz