[Mne_analysis] Volume morphing

[Lori Sanfratello]

        External Email - Use Caution        

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
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
>
> --
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20190412/fbcabe2b/attachment.html