Ping,
If you ever need something more powerful/versatile than shell scripts
and FSLUTILS (Miscellaneous FSL Image Utilities), esp. things you need
to calculate on pixel level, here is a collection of tools (unified by
python) I use, which should achieve almost anything you want to achieve
in matlab (I understand I should refrain myself from commenting on
matlab, but ... anyway):
[1] iPython (interactive env)
[2] PyNIfTI (file I/O)
[3] numpy (number crunching)
[4] rpy2 (interface with R for statistics)
[5] matplotlib (2D plotting)
[6] python-gnuplot (plotting)
If your linux distro is debian, you are lucky because everything is
already packaged for you in the repo.
Regards
Gordon
[1] http://ipython.scipy.org/moin/
[2] http://niftilib.sourceforge.net/pynifti/
[3] http://numpy.scipy.org/
[4] http://rpy.sourceforge.net/
[5] http://matplotlib.sourceforge.net/
[6] http://gnuplot-py.sourceforge.net/
On 02/03/2009 01:49 PM, Eugene Duff wrote:
> Hi Ping,
>
> MATLAB is the most popular tool to quickly perform specific
> calculations. FSL comes with some functions to load and save NIFTII
> images. Many people use bash shell scripting (available from the *nix
> command line) in conjunction with fslmaths etc to perform various
> manipulations of images and other analysis files (see
> https://www.fmrib.ox.ac.uk/fslcourse/lectures/scripting/all.htm).
>
> Best,
>
> Eugene
>
>
> 2009/2/3 WangPing <[log in to unmask] <mailto:[log in to unmask]>>
>
> Dear FSL experts,
>
> I am using fsl for a few months and feeling fsl is a really powerful
> toolkit. I am not an expert of linux and fsl, just curious to know,
> what programming language/tool I should use under linux environment
> (that is compatible with fsl well): for example I want to list and
> read the image volumes processed by fsl, and do some specific
> calculations. Although FSL can provide lots of calculations, just
> want to know what the usual method (for example
> language/tool/script) is to perform some very specific calculations.
>
> Best Regards,
> Ping
>
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>
>
> --
>
> Eugene Duff
>
> FMRIB Centre,
> University of Oxford
> John Radcliffe Hospital, Headington OX3 9DU Oxford UK
>
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>
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