[Nipy-devel] PBrain and nifti

[Thorsten Kranz]

Hi all,

I wanted to inform you that my colleague have addapted loc3d to our needs.
We enabled it to load nifti-images and already used it a couple of times.
It's really a nice program, it makes it really easy to find the precise
positions of the electrodes. Thanks for this nice piece of software.

We also changed the behavior for the export of the electrode positions file.
It now exports two files, one as it did before and one with the coordinates
transformed according to the quaternion-information saved in the nifti-file
so they correspond to the coordinates which fslview gives.

For the import of nifti we had two possibilities: either make it depend on
the nifti-capabilities of nipy of use pynifti.
As we are more used to pynifti, we first chose this way, but it wouldn't be
a huge problem to fix this.

I don't know if these changes are useful for you, but I at least wanted to
inform you that we made them.

Greetings,
Thorsten

2008/1/2, Thorsten Kranz <thorstenkranz@googlemail.com>:
>
> Hi,
>
> this time it's me who has to apologize for the long delay. Over Christmas
> I had little time, so now I finally found time for this E-Mail.
>
> First of all, a happy new year to you all. I hope you had nice holidays.
>
> Now back to business. Actually, I do not want to use PBrain for fMRI
> directly. I'm working on simultanious EEG/fMRI recording, i.e. EEG measured
> directly in the scanner. We want to find correlations between the two
> measurements, and a nice one would also be to find local correlations
> between fMRI-activations and source-localization via the EEG-data. For this,
> it would be very comfy to be able to correctly loacalize the EEG-electrodes
> within the same coordinate-system as the (f)MRI uses.
>
> So, I want to localize the EEG-electrodes within the structural MRI which
> is acquired together with the fMRI-dataset. As I think that the nifti-format
> is quite handy and I use it a lot, I would prefer to be able to use it in
> PBrain instead of always having to do some conversions before.
>
> Greetings,
> Thorsten
>
> 2007/12/20, Michael Castelle <mcc@uchicago.edu>:
> >
> > Hi,
> >
> > Sorry for the long delay in replying. Can you let me know a little more
> > about what you are trying to do with pbrain, and with what kind of
> > datasets? The placement of pbrain in the NIPY project is a little obtuse
> >
> > at the moment, as pbrain is not currently used in practice with fMRI
> > data (just structural MRI data and ECoG recordings). In theory there is
> > no reason why it could not support co-visualization of fMRI activations,
> >
> > but the support is not there yet in the code.
> >
> > mc
> >
> > Thorsten Kranz wrote:
> >
> > > Hi! Once again I have a question...
> > >
> > > I'm trying the pbrain-programms by John Hunter. I think it is'a nice
> > > piece of software and offers many possibilities. I also want to do
> > > some electrode-localization-stuff, and so I would like to work with
> > > it. But, is there a special reason it doesn't support the nifti-format
> >
> > > or didn't just anybody include this possibility yet? If this kind of
> > > help is welcome, I would like to try my luck with this work. Of course
> > > only if you agree with it, John.
> > >
> > > As I already pointed out in my last E-Mail from yesterday, I would
> > > like to use the nifti format, as I use FSL. This would offer great
> > > possibilities to, on the one hand, make use of the abilities of FSL
> > > (like brain-extraction and all this stuff), but on the other hand have
> >
> > > the possibility of full access to the data for individual analysis.
> > >
> > > I'm thankful for any comments, greetings,
> > >
> > > Thorsten
> > >
> > >------------------------------------------------------------------------
> >
> > >
> > >_______________________________________________
> > >Nipy-devel mailing list
> > >Nipy-devel@neuroimaging.scipy.org
> > > http://lists.neuroimaging.scipy.org/mailman/listinfo/nipy-devel
> > >
> > >
> >
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.neuroimaging.scipy.org/pipermail/nipy-devel/attachments/20080404/214437cb/attachment.html