ImScribe – Automated Determination of Imaging Field-of-View
ImScribe works in the following manner:
- It coregisters a “Target localizer” scan (e.g. 1x1x1mm MPRAGE) to a previously acquired “Template localizer”.
- The coregistration information is used to transform a “Template FOV” into “Target” space.
- The coordinates of the “Target” FOV are reported in Siemens prescription terminology (e.g. T>C 23.5 R10.5 P20 H3.5)
- Imscribe supports rigid-body (intra-subject) and affine (inter-subject) and inter-modal (e.g. T1 to T2) coregistration.
- Works directly off Siemens Dicom images or 3D NIFTI volumes.
- Supports single-slice, multi-slice, and 3D data sets
- Supports use of Dicom files from Mosaic EPI, Single Volume Spectroscopy (SVS), or CSI files.
- Can work with ROIs from labelled or thresholded NIFTI files
- Provides visual feedback on registration accuracy and FOV position.
- MATLAB 7.5 (or newer).
- SPM8 (SPM can be obtained from the Wellcome Trust Centre for Neuroimaging at http://www.fil.ion.ucl.ac.uk/spm/ )
- Download the .zip file (see Downloading section below).
- Unzip the files and add them to your Matlab Path.
- Be sure that you have SPM8 installed and in your Matlab path.
- Create data folders to hold the Template, Target and scratch images used/created by Imscribe.
- Edit the imscribe_default_folders.m file to point to the appropriate folders created above.
- Note: the p4 variable in imscribe_default_folders.m must point to a scratch folder with write-permission.
- Run Matlab and type imscribe at the prompt to bring up the Imscribe GUI.
The ImScribe program is available here in a .zip bundle: Download Imscribe (version8 rev1) – updated 10/05/2017.
- Load the required files by clicking the Template Localizer, Template FOV/ROI, and Target Localizer buttons.
- You can select select multiple Dicom files (using the shift-mouse select method), or a single 3D NIFTI file.
- Click the GO button to run the program
- A manual for Imscribe remains to be written…
For comments or questions on the ImScribe program, contact Dr. Mark Elliott.