Hi Lu Feng,<br><br>getting to some voxel-indices to MNI coordinates is a somewhat tricky task. What you have to do is (assuming you have a EPI-sequence, not structural MRI):<br><br>1) coregister your EPI to a structural image of the same subject<br>
2) normalize the structural image to some standard image, e.g. MNI152T1_2mm as contained in fsl data<br>3) apply the concatenated transform EPI->structural an structural->MNI to the EPI sequence<br>4) thus you obtain an image that is in "MNI space", e.g. by opening it in fslview you can find out the MNI coordinates.<br>
<br>Going to Talairach would be the next step, look at<br><br><a href="http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach">http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach</a> <br><br>for more details.<br><br>But be careful: Talairach is not a 1:1 analogy to MNI, some parts of the Tal-Brain are much smaller than in MNI. MNI is an average of 152 brains, Talairach is based on only one example brain.<br>
<br>You do not have to do steps 3+4, after obtaining the two transforms from EPI to structural to MNI, you can also manually calculate MNI coordinates from your voxel coordinates, but I don'T know if you want to do this.<br>
<br>Greetings,<br><br>Thorsten<br><br><br><div class="gmail_quote">2011/11/10 冯璐 <span dir="ltr"><<a href="mailto:fenglu@fingerpass.net.cn">fenglu@fingerpass.net.cn</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
... I can't understand your words exactly ... I used SPM before and I didn't have to think about the voxel space and MNI space, etc. Let's move to some practical problems.<br>
<br>
Loading from<br>
Task1.nii.gz,<br>
I can get<br>
dataset.samples which is a M*N*P matrix.<br>
Using<br>
dataset.mapper.getInId(index),<br>
I can get<br>
a coordinate [z, y, x], x belongs to (0, M), y belongs to (0, N), z belongs to (0, P).<br>
I have checked the result above.<br>
<br>
Using<br>
fslhd Task1.nii.gz,<br>
I can get some information may be useful<br>
qform_name Aligned Anat<br>
qform_code 2<br>
qto_xyz:1 -3.500000 0.000000 -0.000000 76.000000<br>
qto_xyz:2 0.000000 3.500000 -0.000000 -112.000000<br>
qto_xyz:3 0.000000 0.000000 4.000000 -50.000000<br>
qto_xyz:4 0.000000 0.000000 0.000000 1.000000<br>
qform_xorient Right-to-Left<br>
qform_yorient Posterior-to-Anterior<br>
qform_zorient Inferior-to-Superior<br>
sform_name Aligned Anat<br>
sform_code 2<br>
sto_xyz:1 -3.500000 0.000000 0.000000 76.000000<br>
sto_xyz:2 0.000000 3.500000 0.000000 -112.000000<br>
sto_xyz:3 0.000000 0.000000 4.000000 -50.000000<br>
sto_xyz:4 0.000000 0.000000 0.000000 1.000000<br>
sform_xorient Right-to-Left<br>
sform_yorient Posterior-to-Anterior<br>
sform_zorient Inferior-to-Superior<br>
<br>
Then, how can I change the coordinate into a MNI coordinate or a Talairach coordinate?<br>
<br>
Sorry for interruption and thanks in advance.<br>
<div class="im"><br>
Best wishes!<br>
<br>
Lu FENG<br>
<a href="mailto:fenglu@fingerpass.net.cn">fenglu@fingerpass.net.cn</a><br>
<br>
-----Original Message-----<br>
From: pkg-exppsy-pymvpa-bounces+fenglu=<a href="mailto:fingerpass.net.cn@lists.alioth.debian.org">fingerpass.net.cn@lists.alioth.debian.org</a> [mailto:<a href="mailto:pkg-exppsy-pymvpa-bounces%2Bfenglu">pkg-exppsy-pymvpa-bounces+fenglu</a>=<a href="mailto:fingerpass.net.cn@lists.alioth.debian.org">fingerpass.net.cn@lists.alioth.debian.org</a>] On Behalf Of Yaroslav Halchenko<br>
</div><div><div class="h5">Sent: 2011年11月8日 20:55<br>
To: Development and support pf PyMVPA<br>
Subject: Re: [pymvpa] How to export neighborhood relationships of NiftiDataset?<br>
<br>
axes and direction depend on how they are stored in your specific<br>
Nifti -- and those could vary since we do not deduce physical<br>
orientation of the volume anyhow from qform.<br>
<br>
On Tue, 08 Nov 2011, 冯璐 wrote:<br>
<br>
> I think that is what I need.<br>
> So array([0, 0, 1]) is the coordinate in the voxel space. X from 0 to max: right->left; Y from 0 to max: posterior->anterior; Z from 0 to max: inferior->superior ??<br>
<br>
<br>
> Best wishes!<br>
<br>
> Lu FENG<br>
> <a href="mailto:fenglu@fingerpass.net.cn">fenglu@fingerpass.net.cn</a><br>
<br>
> -----Original Message-----<br>
> From: pkg-exppsy-pymvpa-bounces+fenglu=<a href="mailto:fingerpass.net.cn@lists.alioth.debian.org">fingerpass.net.cn@lists.alioth.debian.org</a> [mailto:<a href="mailto:pkg-exppsy-pymvpa-bounces%2Bfenglu">pkg-exppsy-pymvpa-bounces+fenglu</a>=<a href="mailto:fingerpass.net.cn@lists.alioth.debian.org">fingerpass.net.cn@lists.alioth.debian.org</a>] On Behalf Of Yaroslav Halchenko<br>
> Sent: 2011年11月8日 13:35<br>
> To: Development and support pf PyMVPA<br>
> Subject: Re: [pymvpa] How to export neighborhood relationships of NiftiDataset?<br>
<br>
> so we are talking about 0.4.x series of pymvpa (in 0.6 AKA mvpa2 voxel<br>
> indices are explicitly stored in feature attributes of a dataset): so I<br>
> guess you are looking for:<br>
<br>
> In [10]: from mvpa.tests.tests_warehouse import datasets<br>
> In [11]: datasets['3dsmall'].mapper.getInId(0)<br>
> Out[11]: array([0, 0, 1])<br>
<br>
> ?<br>
<br>
> On Tue, 08 Nov 2011, 冯璐 wrote:<br>
<br>
> > Dear experts,<br>
<br>
<br>
<br>
> > I know that using NiftiDataset.map2Nifti() or other functions<br>
> > like mapForward() or mapReverse(), we can deal with either 2D or 3D<br>
> > dataset freely. But I wonder how to export the neighborhood relationships<br>
> > of the volume. Briefly, I��d like to have a transformation matrix or a<br>
> > list of coordinations for each voxel. I need this if I go on with<br>
> > processing by other tools instead of PyMVPA.<br>
<br>
> > Thanks in advanceJ<br>
<br>
<br>
<br>
> > Best wishes!<br>
<br>
<br>
<br>
> > Lu FENG<br>
<br>
> > <a href="mailto:fenglu@fingerpass.net.cn">fenglu@fingerpass.net.cn</a><br>
<br>
<br>
<br>
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=------------------------------------------------------------------=<br>
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