starting.txt

	HELP ON STARTING mrcat (also known as CTMRedit)


I.	What is the command syntax?
II.	Where does mrcat look for the main editable image?
III.	Where does mrcat look for the locator images?
IV.	Quitting mrcat

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I.  What is the command syntax?

	mrcat takes one argument: the name of a directory in which it
should look for image files, e.g.

>> mrcat /home/myhome/mri

	If the directory name is not specified, mrcat will start by
looking in the current directory, e.g.

>> cd /home/myhome/mri;
>> mrcat;

        Note that CTMRedit (as currently implemented) is just an 
alternate name for mrcat, so you can also type

>> cd /home/myhome/mri;
>> CTMRedit;

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II.  Where does mrcat look for the main editable image?

	mrcat recursively searches all subdirectories of the
specified directory until it finds a directory containing image files
which it knows how to load.  The image files mrcat can load include
GE 5.x "MR" files, and all files loadable using the matlab 'imread'
command.

	The first loadable image mrcat finds is loaded as the main
editable image.  The full pathname of this image is parsed as follows,
and the popup menus beneath the main editable image are intialized
accordingly (see the file "Help on Image Loading").

PATH = ROOTDIR/<ImageType>/<ImageSeries>/<ImagePlane>/<ImageFile>

	If no editable images are found in any subdirectory of the
directory specified on the command line, then mrcat will go up JUST
ONE directory level, and search the subdirectories of all "brothers
and sisters" of the specified directory.

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III.  Where does mrcat look for the locator images?

	Once the main editable image is found, mrcat looks for
sagittal locator images in subdirectories of

	ROOTDIR/<ImageType>/<ImageSeries>/<SagPlane>

	Where <SagPlane> is by default the character 's'.  If no
images are found in this directory, mrcat will test all of the 
possible values of <ImageSeries>.  This can be useful, for example,
if you only want to keep sagittal locator images in the one directory

        ROOTDIR/<ImageType>/_loc/s

	Likewise, the coronal/axial locator image is sought beneath

	ROOTDIR/<ImageType>/<ImageSeries>/<CorAPlane>

	If <ImagePlane> is 'c', <CorAPlane> is initially 'a',
otherwise <CorAPlane> is initially 'c'.

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IV.  Quitting mrcat

	First, if you have made any changes to the outline, save your
changes by pressing the "Save Otl" button.

	Now you can quit by pressing the "Close" button.

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