[pymvpa] load raw 'not nifti' data

[Michael Waskom]

Does the make_average_subject routine guarantee that the surface can be
reshaped to fit into Nifti?  If so, it's probably easiest to just stick the
timeserieses together in a reshaped nifti and read that in with Nibabel.

Or feel free to just steal the read_scalar_data function from the PySurfer
source.  It's quite simple :)

https://github.com/nipy/PySurfer/blob/master/surfer/io.py#L108

Best,
Michael

On Wed, Oct 5, 2011 at 6:59 PM, Gregory Kirk <gkirk at wisc.edu> wrote:

> 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.
> >
> >
> >
> >
> >
> > The other upside of installing PySurfer is that you can then display
> pretty MVPA results with a lot more flexibility than tksurfer offers you :)
> >
> >
> > Best,
> > Michael
> >
> >
> >
> >
> >
> > On Tue, Oct 4, 2011 at 7:02 PM, Yaroslav Halchenko <
> debian at onerussian.com <debian at onerussian.com>> wrote:
> >
> > >
> >
> > >
> >
> > > another possible (haven't tried... unfortunately I am still
> ignorant in
> > >
> >
> > > FreeSurfer ;) ) way is
> > >
> >
> > >
> > >
> >
> > >  sudo apt-get install python-surfer
> > >
> >
> > >
> > >
> >
> > > and then in python
> > >
> >
> > >
> > >
> >
> > >   from surfer.io(http://surfer.io) import read_morph_data
> > >
> >
> > >   x =  read_morph_data(filename)
> > >
> >
> > >
> > >
> >
> > > and then combined them into dataset as Per mentioned.
> > >
> >
> > >
> > >
> >
> > > On Tue, 04 Oct 2011, Per B. Sederberg wrote:
> > >
> >
> > >
> > >
> >
> > > > Hi Greg:
> > >
> >
> > >
> > >
> >
> > > > You can save out that big matrix to a mat file from matlab (say the
> > >
> >
> > > > matrix is named mymat and you save it to mymatrix.mat) and then read
> > >
> >
> > > > it in with:
> > >
> >
> > >
> > >
> >
> > > > import scipy.io(http://scipy.io)
> > >
> >
> > > > x = scipy.io.loadmat('mymatrix.mat')['mymat']
> > >
> >
> > >
> > >
> >
> > > > Then in pymvpa (depending on the version you are using) you can get
> it
> > >
> >
> > > > ready for business with:
> > >
> >
> > >
> > >
> >
> > > > from mvpa.suite import *
> > >
> >
> > >
> > >
> >
> > > > dat = dataset_wizard(x, targets=cov_of_interest,
> chunks=range(len(x)))
> > >
> >
> > >
> > >
> >
> > > > Then you can can start analyzing away...
> > >
> >
> > >
> > >
> >
> > > > Best,
> > >
> >
> > > > Per
> > >
> >
> > >
> > > --
> > >
> >
> > > =------------------------------------------------------------------=
> > >
> >
> > > 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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> > >
> >
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> > >
> >
> > >
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> > >
> >
> > >
> > >
> > >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
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