ImScribe – Automated Determination of Imaging Field-of-View
ImScribe is designed to allow reproducible selection of the same anatomical Field-of-View in Siemens MRI studies. The program is written in Matlab and requires the installation of the SPM software toolbox (see Requirements below). It is specifically intended for group studies in neuroimaging applications (like fMRI) where reproducible acquisition of the same anatomical brain region is desired. The program is specific to the Siemens Dicom imaging format and method of specifying imaging FOVs.
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 (version9) – updated 05/2021.
- 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.