[pymvpa] load raw 'not nifti' data

[Gregory Kirk]

i use the ' old way' in freesurfer, so i made an average surface with make_average_subject, then resampled allmy subjects onto it with mris_preproc and the resulting file is in .mgh format.


i know i can load the data into a matlab matrix with a freesurfer matlab script, i am forced to use
the redhat derived scientific linux as that is what is installed by the IT guys for us. so earlier today
i had an e-mail with Yarik about the C++ compile errors i was getting and he was going to get back to me.
so at the moment maybe installing the Pysurfer module may not be as easy for me as i cant just apt-get install
and be sure it will go smooth, so for a first crack
im hoping the load matlab mat  method that i got in an earlier e-mail from the list may be more simple, although
as i get rolling maybethe viewer you suggest sounds interesting.


thanks, ill be in touch once i get the basic PyMVPA running


cheers


Greg

On 10/05/11, Michael Waskom   wrote:
> As I understand the question, you want to use morphometric data that's been transformed into some standard space (i.e. you've run recon-all -qcache), so actually you wouldn't use read_morph_data (which only applies to the morphometric data files in the format that gets spit out of recon-all) but rather read_scalar_data, which will read in either Freesurfer .mg{hz} files (which is probably the format your data are in) or anything that's readable by nibabel.  Note that it will always just return a vector of datapoints matching the vertices in surface the scalar data file, even if the underlying data is a "reshaped" nifiti file which is probably what you want anyway if you're sticking it together into a dataset sample matrix.
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> The other upside of installing PySurfer is that you can then display pretty MVPA results with a lot more flexibility than tksurfer offers you :)
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> Best,
> Michael
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> On Tue, Oct 4, 2011 at 7:02 PM, Yaroslav Halchenko <debian at onerussian.com <debian at onerussian.com>> wrote:
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> > 
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> > another possible (haven't tried... unfortunately I am still ignorant in
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> > FreeSurfer ;) ) way is
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> >  sudo apt-get install python-surfer
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> > and then in python
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> >   from surfer.io(http://surfer.io) import read_morph_data
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> >   x =  read_morph_data(filename)
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> > and then combined them into dataset as Per mentioned.
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> > On Tue, 04 Oct 2011, Per B. Sederberg wrote:
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> > > Hi Greg:
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> > > You can save out that big matrix to a mat file from matlab (say the
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> > > matrix is named mymat and you save it to mymatrix.mat) and then read
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> > > it in with:
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> > > import scipy.io(http://scipy.io)
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> > > x = scipy.io.loadmat('mymatrix.mat')['mymat']
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> > > Then in pymvpa (depending on the version you are using) you can get it
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> > > ready for business with:
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> > > from mvpa.suite import *
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> > > dat = dataset_wizard(x, targets=cov_of_interest, chunks=range(len(x)))
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> > > Then you can can start analyzing away...
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> > > Best,
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> > > Per
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> > 
> > --
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> 
> > =------------------------------------------------------------------=
> > 
> 
> > Keep in touch                                     www.onerussian.com(http://www.onerussian.com)
> > 
> 
> > Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic(http://www.ohloh.net/accounts/yarikoptic)
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> > _______________________________________________
> > 
> 
> > Pkg-ExpPsy-PyMVPA mailing list
> > 
> 
> > Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org <Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org>
> > 
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> > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
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