[Mne_analysis] Volume morphing

[Lori Sanfratello]

        External Email - Use Caution        

Thank you!  I can open the morphed nifti files that come out of MNE-python
in freeview on top of the anatomy and they look reasonable (e.g. fill the
entire anatomy).  I then take these nifti files and feed them into an ICA
and the components that come out are what does not quite fill the entire
brainspace.  I have done something similar, in a very round-about fashion
with surface morphing (and then projection into the volume) before the
volume morphing was available and did not encounter this issue.  One other
note, I seem to remember somewhere in the process an objection that the
units weren't set/or weren't recognized, but it still processed...
Best, Lori

On Thu, Apr 11, 2019 at 8:23 AM Eric Larson <larson.eric.d at gmail.com> wrote:

>         External Email - Use Caution
>
> It's possible that there is some bug with the transformations, or the
> visualization (we are sorting through some things that could be related in
> a volume viz PR <https://github.com/mne-tools/mne-python/pull/6046>
> currently). Can you try to replicate this problem using some minimal
> example? I would start by seeing if it can be replicated without the
> ICA-component step, for example by morphing some activity and visualizing
> it to see if it also fails to fill the brain. If this shows the problem
> already, you can share the original MRI, destination MRI, original
> activation, and code to generate and visualize the morphed activation.
>
> It's best if this can be done with the `sample` dataset (e.g.,
> sample->fsaverage), so try to replicate there, too -- it'll make sharing
> and testing easier. But I'm guessing it won't show the problem because
> sample and fsaverage have the same data orientation, zooms, etc., which
> might not be the case for your data.
>
> Eric
>
>
> On Wed, Apr 10, 2019 at 6:08 PM Lori Sanfratello <lsanfratello at mrn.org>
> wrote:
>
>>         External Email - Use Caution
>>
>> Hi, I have been using MNEs volume morphing, but I seem to be running into
>> an issue where when I try to use the nifti output with an ICA program: the
>> ICA components don't quite "fill" the brain...? I believe I am using python
>> 2.7.15 and mne 0.17.0 to create the files.  Thank you for any advice, Lori
>>
>> --
>> Dr. L. Sanfratello, PhD
>> Assistant Professor of Trans. Neuroscience
>> The Mind Research Network,
>> 1101 Yale Blvd NE
>> Albuquerque, NM 87106
>> 505 272-5557
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-- 
Dr. L. Sanfratello, PhD
Assistant Professor of Trans. Neuroscience
The Mind Research Network,
1101 Yale Blvd NE
Albuquerque, NM 87106
505 272-5557
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