[Mne_analysis] Volume morphing

Lori Sanfratello lsanfratello at mrn.org
Fri Apr 12 16:29:48 EDT 2019
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Apologies, it was an issue with the masking, nothing to do with MNE.
Thanks for working with me to try and figure it out!
Best,
Lori

On Thu, Apr 11, 2019 at 9:22 AM Lori Sanfratello <lsanfratello at mrn.org>
wrote:

> 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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>>> Mne_analysis mailing list
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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
>


-- 
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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