[pymvpa] How to export neighborhood relationships of NiftiDataset?

[冯璐]

Dear Yaroslav,

	Thank you for your response. It's helpful. But I still have several questions.
	Q1. dataset.mapper.getInId(index) --> [x,y,z] --> X from 0 to max: right->left; Y from 0 to max: posterior->anterior; Z from 0 to max: inferior->superior ??
	Q2. After detrending, the intensities of some voxel across the entire run become zeros. That means dataset has some columns full of zeros. Why??
	Q3. Because of Q2, I checked the coordinates of the voxels whose values were zeros across the entire run after detrending. I entered the coordinates in the FSLView. (Can I do like this??) I found that some voxels were out of the mask by which I extract the dataset. Why?? Did I do something improper? Or is it a bug?

	Thanks in advance and any help will be appreciated.

Best wishes!

     Lu FENG
fenglu at fingerpass.net.cn


-----Original Message-----
From: pkg-exppsy-pymvpa-bounces+fenglu=fingerpass.net.cn at lists.alioth.debian.org [mailto:pkg-exppsy-pymvpa-bounces+fenglu=fingerpass.net.cn at lists.alioth.debian.org] On Behalf Of Yaroslav Halchenko
Sent: 2011年11月8日 13:35
To: Development and support pf PyMVPA
Subject: Re: [pymvpa] How to export neighborhood relationships of NiftiDataset?

so we are talking about 0.4.x series of pymvpa (in 0.6 AKA mvpa2 voxel
indices are explicitly stored in feature attributes of a dataset):  so I
guess you are looking for:

In [10]: from mvpa.tests.tests_warehouse import datasets
In [11]: datasets['3dsmall'].mapper.getInId(0)
Out[11]: array([0, 0, 1])

?

On Tue, 08 Nov 2011, 冯璐 wrote:

>    Dear experts,

>     

>             I  know that  using NiftiDataset.map2Nifti()  or other  functions
>    like mapForward()  or mapReverse(),  we  can deal  with  either 2D  or  3D
>    dataset freely. But I wonder how to export the neighborhood  relationships
>    of the volume.  Briefly, I��d like  to have a  transformation matrix or  a
>    list of  coordinations  for each  voxel.  I need  this  if I  go  on  with
>    processing by other tools instead of PyMVPA.

>             Thanks in advanceJ

>     

>    Best wishes!

>     

>         Lu FENG

>    fenglu at fingerpass.net.cn

>     

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