[pymvpa] load raw 'not nifti' data

Gregory Kirk gkirk at wisc.edu
Thu Oct 6 06:51:10 UTC 2011


no it cannot be fit into a nifti, it is only cortical surface values not volume information ( 2D information).there are n_subjects x n_cortical_thickness_values ,in this case 60 x ~200,000




it needs to be imported into an object with 60 samples each with 200,000 features.


greg

On 10/05/11, Michael Waskom   wrote:
> 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.
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> Or feel free to just steal the read_scalar_data function from the PySurfer source.  It's quite simple :)
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> https://github.com/nipy/PySurfer/blob/master/surfer/io.py#L108
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> Best,
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> On Wed, Oct 5, 2011 at 6:59 PM, Gregory Kirk <gkirk at wisc.edu <gkirk at wisc.edu>> wrote:
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> > 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.
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> > i know i can load the data into a matlab matrix with a freesurfer matlab script, i am forced to use
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> > the redhat derived scientific linux as that is what is installed by the IT guys for us. so earlier today
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> > i had an e-mail with Yarik about the C++ compile errors i was getting and he was going to get back to me.
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> > so at the moment maybe installing the Pysurfer module may not be as easy for me as i cant just apt-get install
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> > and be sure it will go smooth, so for a first crack
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> > im hoping the load matlab mat  method that i got in an earlier e-mail from the list may be more simple, although
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> > as i get rolling maybethe viewer you suggest sounds interesting.
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> > thanks, ill be in touch once i get the basic PyMVPA running
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> > cheers
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> > Greg
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> > On 10/05/11, Michael Waskom   wrote:
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> > > 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,
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> > > Michael
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> > > On Tue, Oct 4, 2011 at 7:02 PM, Yaroslav Halchenko <debian at onerussian.com <debian at onerussian.com> <debian at onerussian.com <debian at onerussian.com>>> wrote:
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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)(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)(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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> > > > =------------------------------------------------------------------=
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> > > > Keep in touch                                     www.onerussian.com(http://www.onerussian.com)(http://www.onerussian.com)
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> > > > Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic(http://www.ohloh.net/accounts/yarikoptic)(http://www.ohloh.net/accounts/yarikoptic(http://www.ohloh.net/accounts/yarikoptic))
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> > > > _______________________________________________
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> > > > Pkg-ExpPsy-PyMVPA mailing list
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> > > > Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org <Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org> <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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> > > _______________________________________________
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> > > Pkg-ExpPsy-PyMVPA mailing list
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> > > 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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> > _______________________________________________
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> > Pkg-ExpPsy-PyMVPA mailing list
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> > 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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