FSL, Freesurfer, and SPM are all free tools to analyze MRI images. MRIcron also has a dcm2nii conversion that is very nice. Beyond SPM, matlab also has a number of toolboxes for converting and visualizing images

http://www.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image

http://www.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter

http://www.mathworks.com/matlabcentral/fileexchange/22508-siemens-dicom-sort-and-convert-to-nifti

http://www.mathworks.com/matlabcentral/fileexchange/22508-siemens-dicom-sort-and-convert-to-nifti

Hi

There is no free toolbox for Matlab. The study and manipulation of MRI stuffs might be done under aegis of pattern recognition and image processing toolbax in matlab. one can dig into the neural properties of MRI, as the other approach. Matlab, as you probably know, has a NN toolbox to model sigmoidal NN. If you're going to take the spiking dynamics of the brain into account, you can use python driven packages for spiking NN just like PyBrain, neurolab and FANN.

A coherent list might be found as below:

https://wiki.python.org/moin/PythonForArtificialIntelligence

Best

Thank you

Do you mean something like SPM? or brainstorm! or freesurfer matlab scripts! What do you want to do exactly?

FSL, Freesurfer, and SPM are all free tools to analyze MRI images. MRIcron also has a dcm2nii conversion that is very nice. Beyond SPM, matlab also has a number of toolboxes for converting and visualizing images

http://www.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image

http://www.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter

http://www.mathworks.com/matlabcentral/fileexchange/22508-siemens-dicom-sort-and-convert-to-nifti

http://www.mathworks.com/matlabcentral/fileexchange/22508-siemens-dicom-sort-and-convert-to-nifti

Try SPM for registration.

I would also check the http://www.sci.utah.edu/. You can find there many open source tools for handling dicom files.

Also try registration and segmentation tools in the latest "3D Slicer 4.3".

You could try our new online platform for automatic MRI brain analysis.

Our web based pipeline is called "volBrain" and can be accessed at this address:

http://volbrain.upv.es

volBrain is able to produce volumetric information of different brain tissues/structures in a fully automatic way in around 15 minutes. The way it works is very simple; you have just to register as a new user in the system and to upload a single anonymized compressed T1w brain MRI in nifti format. You will receive an email with a pdf/csv summarising the results and you will be able also to download the resulting label files and images in your user area using your account.

Our aim is to provide a simple and free tool that can be used no matter where you are without any installation or computer requirements. Since we want to make the tool available to the higher possible number of users, a limit of 5 cases per day/user has been set.

We encourage you to register in the system and to use it. We will be very grateful if you can provide us your comments/suggestions in order to improve the system.

Good luck in your research!!

Jose V. Manjon and Pierrick Coupe

Hello, I have two suggestions if you are analysing 3D data:

1) The Matlab viewer3d can display 3D volumes with Maximum Intensity Projection, transparency, etc. There are functions to load DICOM data (in ReadData3D sub-folder). I don't know if there are registration functions though.

http://www.mathworks.com/matlabcentral/fileexchange/21993-viewer3d

2) The vaa3D 3D visualization software can display volume stacks in 3D (MIP, Alpha Blending Projection, etc). It has plug-ins for brain analysis ("brain connectome mapping", "3D deformable registration", "3D neuron tracing/reconstruction", "3D neuron structure comparison" - from the documentation). I don't see DICOM in the import options, but there is a load_image_using_Bioformats plug-in, so it should be possible to load DICOM data. And if you are interested in an easy way to share data with Matlab, there is also a Matlab Input/Output Toolbox (I couldn't manage to compile the MEX files in Windows, but it seems to work on Mac/Linux).

In the "related tools", there is also mention of BrainAligner.

http://home.penglab.com/proj/vaa3d/home/index.html

http://penglab.janelia.org/proj/brainaligner/BrainAligner/Download.html

FSL (complied), ANTS (compiled), SPM (matlab or compiled)

Note that most toolboxes won't work directly with dicom images (there's want something like Analyze of Nifti formats). You may use dcm2nii tool to convert your images to nifti format, to get the ball rolling.

I reviewed reconstruction algorithms in the following publication:

Conference Paper A REVIEW OF RECENT RANGE IMAGE RECONSTRUCTION ALGORITHMS