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From ctfsamout

CTF-SAM-OUT is in Beta now!

Contents 1 Where is the beef? 2 System requirements 3 Setting up 4 What's next? 5 Known bugs 6 DO NOT USE IT, SOMETIMES 7 Disclaimers 8 Another run of slogans

Where is the beef?

• This is the wiki main page, boring, no pictures. If you want some pictures, take a look at snapshots.
• The project summary page is here.
• If you want to download it, go to here.

System requirements

• A Linux machine, e.g., Ubuntu or openSUSE (Yes, you have to use Linux. Not even Mac OS X. We will embrace Mac users soon. But we will never write a toolbox for Windows to extend the life of the evil operating system.)
• MATLAB(just itself).
• SPM, a MATLAB toolbox.
• REST (version = 1.4), a MATLAB toolbox which we will dump soon.
• AFNI, a toolbox that any computational neuroscientist knows.
• 3dNormalize, a UNIX Shell script provided by NIMH MEG Core Facility.

Setting up

1. Install all things above according to their own installation instructions. Do necessary things, such as set MATLAB Path or PATH environment variable on Linux.
2. Download our code, which is a tar.bz2 ball. Check the date. Be sure to get the latest one. Extract it. Do not forget to add the extracted folder into your MATLAB path if it is not your working directory.
3. Download our testing data if you like. And place the test data in the same directory of extracted code.
4. Type and run make on your Linux shell (i.e., terminal). It will automatically compile all C codes.
5. Type and run help ctf_sam_out on MATLAB Command Window to learn how to use it. If THRESHOLD is smaller than the minimum value in your SAM result, it will be ignored.
6. To run the test data, find the run.m and run it (just type run in MATLAB prompt at proper directory). We have the filenames for our testing data filled for you. You may change it to your own SAM result file (of suffix .svl) and CTF-format MRI image (of suffix .mri).

What's next?

• Enjoy registering and superposing SAM result from CTF workstation with MRI image.
• Report bugs to us, using mailing list, forum, email, tracker or any sort of super natural power.
• Come back some time to see whether we have fixed the bugs.

Known bugs

• Our capture.sh cannot handle file names that contain more than one dots, including ... So please place your data in the same path (i.e., directory, folder) with our programs.
• The output file name has to be out.mri. We will modify the writeMRI.c soon.
• On some Ubuntu versions, e.g., 9.10, the default /bin/sh which is dash cannot properly interpret our Shell scripts. Please force to use bash.

DO NOT USE IT, SOMETIMES

This software is intended for research and educational purpose only. Do NOT use it on medical devices, especially those critical to life, such as surgical imaging navigation system, nor for making any diagnostic decisions. Programmers of this software are human beings that can make mistakes.

Disclaimers

1. This project has nothing to do with CTF company.

Another run of slogans

This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
     any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see http://www.gnu.org/licenses/.