MRIcro tutorial

参考网址：http://www.mccauslandcenter.sc.edu/mricro/mricron/

　　　　　http://www.cabiatl.com/mricro/mricro/mricro.html

This guide gives is a brief description of how you can use MRIcro and SPM to work with patient scans. For the MRIcro manual and software, visit the MRIcro home page (also available at www.icn.ucl.ac.uk/groups/jd/mricro/mricro.html). I also keep a have a FAQ that describes some of the more unusual features of MRIcro. Information about SPM can be found atwww.fil.ion.bpmf.ac.uk/spm/, or at www.mrc-cbu.cam.ac.uk/Imaging/. This tutorial will describe the following features:

Downloading this tutorial

Windows users can download this tutorial by downloading the Windows installer.
Linux users can download a zip file: shift+click here. This will copy a compressed version of the MRIcro web pages ('mritut.zip') to your computer (The zipped file requires around 450 kb).
The MRIcro installation include a 1x1x1mm MRI scan. This is useful for learning how to use MRIcro. The image is named 'ch2bet.img': this is scalp-stripped version of the average of 27 T1-weighted scans of the same individual as displayed at www.bic.mni.mcgill.ca/cgi/icbm_view). A version of this image with the scalp included is also included with the latest MRIcro releases (this file is named ch2.img). Note that this MNI image does not exactly match the Talairach atlas. However, an MNI atlas is available.

Viewing an image

Select 'Open Analyze Format hdr+img...' from the 'File' menu. You will be asked to select the MRI you wish to view. At the Medical Research Council, the (normalized) T1 scans have the name 'n'+scan number (e.g. n12345) while the T2 ('pathological') scans have the name 'p'+ scan number (e.g. p12345).
The 'slice viewer' panel has three sliders: the top slider determines the scan slice you will be shown.

Left: The 'Slice viewer panel'. Controls on this panel allow you to adjust the appearance of the image you have opened.
You can use the 'black' and 'white' sliders to adjust the brightness of the image. An automated brightness can be selected by selecting 'Contrast autobalance' from the 'View' menu. With some images (those with more than 256 levels of gray), adjusting the brightness sliders will cause the 'optimise contrast' button to appear (in the figure above, it is the black and white circle). Selecting 'Contrast autobalance' from the 'View' menu usually improves the image's appearance.
The bottom of the slice viewer panel allows you to select the cut you wish to view (transverse, sagittal, coronal, projection, free rotate or multiple slice views are available).
An easy way to view an image is to select the projection view, and then click on the brain image to select the coordinates you wish to view.

Creating a region of interest

Run MRIcro and select 'Open Analyze Format hdr+img...' from the 'File' menu. Enter the name and path of the file you wish to view.

You will probably only want to create a region of interest on the T1 weighted scan, but you may want to open up a T2/proton density/T2* image to check the lesion location. For more information on different types of MRI scans, visit Joseph P. Hornak's The Basics of MRI web page. The Whole Brain Atlas also has examples of MRI/CT data.

Left: T1, proton density and T2 weighted slices from the same patient. The 'pathological' T2 scan is useful for locating the lesioned region in the brain. The 'anatomical' T1 scans usually have the best scan resolution, and are useful for localizing anatomical structures. The PD scan shows overall hydrogen density per cubic mm. Note artifacts caused by an aneurysm clip located directly anterior to the lesion (black hole, with a white halo in these images).

Right: Relative brightness levels for different material in T1 and T2 scans. Notice that lesions are generally bright in T2 scans.

Regions of interest can only be drawn on the transverse, coronal and sagittal slices of the images (MRIcro versions prior to 1.20 only allow ROIs to be defined on the transverse slices). In the slice viewer panel, click on the button that shows a minature axial view of the brain. If the image does not appear to be sliced axially when the transverse button is selected (e.g. the scan looks coronal), then you may want to rotate the image, as described in the next section.
Press F3 to select the closed pen (or click on this tool in the region of interest panel).

Left: Drawing a region of interest on a scan.
Go to the slice you wish to edit (you can use the F1 and F2 keys to go to the next lower or higher slice, respectively)
Draw the region of interest by dragging the mouse cursor around the border while depressing the left mouse button.
Go to the center of the region, an click the right mouse button to fill the region.
If you make a mistake, press the icon of the hand holding an upside down pencil (it is in the region of interest panel). This will erase your region of interest from this slice only. You can also shift-click to delete a region of a ROI. For example, shift-left-clicking deletes a region of interest beneath the mouse's movements, while shift-right clicking deletes a filled-region underneath the mouse's position.
Repeat steps 5-8 until you have drawn the lesion on all of the slices.
Choose 'Save ROI...' from the 'ROI' menu. It is often useful to give the ROI the same name as the image file (e.g. if the image file is n12345.img then the roi should be as n12345.roi).
Open the next image you wish to view. Repeat until you have created region of interest information for all of the images you want to process.

Note: MRIcro 1.36 and later includes tools for creating intensity-defined 3D regions of interest.

Segmenting a region of interest

MRIcro can also be used to filter a region of interest based on the image intensity of the scan. For example, consider an fMRI study of auditory cortex. The experimenter has drawn a region of interest to delineate this region of the cortex, but is specifically interested if the activity of the gray matter is modulated with the task. To solve this problem, the experimenter could filter the ROI of auditory cortex in order to remove white matter from the analysis. Note that SPM99 has a series of sophisticated segmenting algorithms that may be more accurate than MRIcro in many instances. MRIcro can apply an intensity filter to the entire volume (so the same contrast levels are applied to all of the slices in the entire image), to a single slice or to a region within a single slice.

Here is a step-by-step guide for segmenting an ROI using MRIcro: