Dear all
I am looking for a tool to calculate SWI images based on magnitude and phase susceptibility images
I found one tool which is based on Matlab http://fmri.ucsd.edu/Howto/swi.shtml
But I would prefer a tool for FSL or a standalone tool without the need for matlab
Are there any existing tools available?
Thanks !!
Dear
Look the link. May be useful.
http://www.cs.ukzn.ac.za/~hughm/ai/readings/PrologIntro.pdf
Regards, Shafagat
Shafagat, I'm sure he's not referring to the Prolog programming environment from the Swedish Institute. He's referring to susceptibility weighted imaging (SWI) which is an MRI method.
Sven, here are two links:
http://www.weill.cornell.edu/mri/pages/qsm.html
http://www.mrimaging.com/category.88.html
Yes indeed - susceptibility weighted imaging (SWI)!
Thanks you very much Shafagat & Arastoo for your answers !!
Sven
Dear Swen, what about QSM? Neuroimage. 2012 Sep;62(3):1593-9. doi: 10.1016/j.neuroimage.2012.05.049. Epub 2012 May 24. Radiology. 2013 May;267(2):551-9. doi: 10.1148/radiol.12120707. Epub 2013 Jan 11. it is based on FSL. Klaus
Dear Klaus
Thanks a lot for your message
I agree, QSM is certainly a very interesting technique, but at this stage probably more for a research setting. This will hopefully change in the future :-)
Currently, I have a very simple clinical problem. I used to work on Siemens and like the SWI contrast for clinical applications. Now I changed position and we now have GE. The SWAN images provide magnitude and phase images, yet (at least on our implementation), there is not SWI contrast calculation. It would be nice to have this for clinical reasons. This also means that it should be calculated directly on the scanner, as it is not practical for clinics to export the data on another computer etc.
Thanks
Sven
Hi Sven,
Calculating SWI from magnitude and phase is not very difficult. I suggest you implement it first in Matlab or Python and then you try to get the scanner to do the calculation. I guess getting the scanner to do it is harder than figuring out the algorithm off-line.
You probably get multi echo data, so you may want to read Denk and Rauscher JMRI 2010. An essential paper is Reichenbach et al. Radiology 1997.
Cheers,
Alex
Hi Sven,
I would recommend using SPIN Software designed by Prof. Haacke Group at Wayne State University.
http://www.mrc.wayne.edu/download.htm
Ali
http://mrinnovations.com/ should have a link to SPIN-LITE and a research version with additional modules called SPIN-PRO.
For those looking to find software reconstruction tools for SWI, all the links provided by the other answers do not work anymore as of 2020, the softwares are either dead or even if they can be retrieved (such as swi_v2 https://web.archive.org/web/20200226130140/http://fmri.ucsd.edu/download/swi_v2.tar ), they do not work with nifti files but with defunct image formats, and since they are not opensource, we can't fix that.
Fortunately, Korbinian Eckstein made an amazing opensource implementation in Julia in the SWI.jl package: https://github.com/korbinian90/SWI.jl
It can reconstruct both the SWI and SWI-mIP from just the raw magnitude and phase images. It works very well and even supports multi-echo SWI.
An alternative is to use FSL's PRELUDE, which is the most accurate method of reconstruction for phase images as described in: Article Quantitative Assessment of Susceptibility-Weighted Imaging P...
However with this last option, you will have to calculate manually the rest of the pipeline, such as mixing the magnitude with the filtered phase image, and then compute the minimum intensity projection (an example pipeline for FreeSurfer and using PRELUDE for preprocessing can be found here: https://github.com/ksubramz/SWI_Processing ).
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