[pymvpa] Fwd: Data import with pynifti

[Roberto Guidotti]

Hi Yaroslav,

I'm a novice of fMRI and MVPA Analysis, I think you want to know if those
fields are congruent with Analyze format specially if they are from SPM.
Well, the files I have are converted using Brain Voyager, so viewing the
file you link it shouldn't have that problem.
Checking my images with MRIcro and viewing fields on PyMVPA with command
mydataset.niftiheader.get() (Images loaded by list of NiftiImages!) I found
the same values:
scl_interp = 19 e scl_slope = 17; now my question is: Could I proceed with
the analysis or I have to do other further steps?

Thank you
Roberto


2011/3/3 Yaroslav Halchenko <debian at onerussian.com>

Hi Roberto,
>
> as we have discovered in our troubleshooting thread with Nynke van der
> Laan, in PyMVPA  0.4.x and 0.5.x series, while relying on pynifti
> interface to load data, we did not account for scaling/offset parameters
> encoded in Nifti headers.  So, if those .hdr/.img correspond to Nifti
> files, you should better check if they have the same scl_inter/scl_slope
> values... if those correspond to Analyze files... it is even more
> interesting since then if it comes from SPM, according to
>
> http://nifti.nimh.nih.gov/nifti-1/documentation/Analyze_usage.pdf
>
> those inter/slope could still have been encoded in some fields, and thus
> loaded data might not be appropriate for the analysis in PyMVPA.  The
> best resolution would be to join them into a single 4D Nifti
> volume file (and double check if scaling/offsetting is done correctly by
> the software you would use for that)
>
> Tomorrow or on weekend we will make full announcement and fresh
> bugfix release of 0.4.x series which should take care about scaling
> issue.
>
> Meanwhile -- if you have 'Analyze' files -- would you mind forwarding me
> few samples to check on the status of their fields.
>
> With best regards,
> Yarik
>
> On Thu, 03 Mar 2011, Roberto Guidotti wrote:
>
> >    Thank you Michael it works perfectly....
> >    Sorry but I'm a novice with Python and this technique, I'm glad to
> have
> >    the support of you and the other authorities of MVPA techniques!!
> >    Thank you
> >    Roberto
>
> >    2011/3/1 Michael Hanke <[1]michael.hanke at gmail.com>
>
> >    On Mon, Feb 28, 2011 at 04:38:58PM +0100, Roberto Guidotti wrote:
> >    > Dear all,
>
> >    > I have to analyze some fmri data with pymvpa: my images are in
> >    Analyze
> >    > format: every volume is a .hdr .img pair and I have to load as a
> time
> >    > series. How can I do?
> >    > The solution is to convert my datasets with some software as MRIcro
> >    or
> >    > similar, but I want to know if there is a "library" solution to
> solve
> >    that
> >    > issue or if I could do this by building a script managing and
> merging
> >    > several arrays.
>
> >      You should be able to load them all one by one into a list of images
> >      and
> >      supply that list as an argument to the Dataset constructor. It
> >      should
> >      just work.
> >      Michael
> >      PS: Sorry for the delay
> --
> =------------------------------------------------------------------=
> Keep in touch                                     www.onerussian.com
> Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic
>
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