[Mne_analysis] hcp-mne head_mri trans

[Denis-Alexander Engemann]

        External Email - Use Caution        

Yes I think I tilted the display a bit for aesthetics. Can you just try the
tutorial code for a few cases yourself to see if you get convinced?
I have been so far pretty convinced that we got the transforms right and
the source localizations look plausible.
We may want to document this better ...

Best,
Denis

On Fri, Jan 11, 2019 at 6:03 PM Maximilien Chaumon <
maximilien.chaumon at gmail.com> wrote:

>         External Email - Use Caution
>
> ok. So I assume things are just fine.
> Only the device helmet, represented in blue in the figure is somehow
> tilted 90° off, but it's just an aesthetic thing if I understand correctly,
> right?
>
> Le ven. 11 janv. 2019 à 17:46, Denis A. Engemann <
> denis-alexander.engemann at inria.fr> a écrit :
>
>>         External Email - Use Caution
>>
>> Hey Max,
>>
>> Checkout this tutorial:
>> http://mne-tools.github.io/mne-hcp/auto_examples/plot_coregistration.html#sphx-glr-auto-examples-plot-coregistration-py
>>
>> The default mne plotter does not work. You need to manage the hcp
>> transforms differently from how mne thinks it should be done.
>>
>> Let me know if it helps.
>>
>> Denis
>>
>> On 11 Jan 2019, at 17:38, Maximilien Chaumon <
>> maximilien.chaumon at gmail.com> wrote:
>>
>>         External Email - Use Caution
>>
>> Hello,
>>
>> I'm starting to play around with mne-hcp
>> I'm picking code in the examples of mne-hcp to create in each subjec:
>> mne_anatomy. fine
>> bem_model and _solution. fine
>> head_mri_t. fine
>> check that everything is in place with mne.viz.plot_alignment, and I get
>> this:
>> https://drive.google.com/open?id=17altWLQIfyZMxUcvnsxgzJp9zN0qcET0
>> I understand that the head_mri_t is not applied to the helmet. is that
>> correct? how impactfull is that for upcoming computations? how can I fix it?
>>
>> Many thanks,
>> Max
>>
>> This is my code:
>>
>> import os.path as op
>> import glob
>> import mne
>> import hcp
>>
>> storage_dir =
>> op.expanduser('~/owncloud/Lab/Projects/SOLID_MEEG/data/HCPunzipped')
>> subjects_dir =
>> op.expanduser('~/owncloud/Lab/Projects/SOLID_MEEG/data/HCPsubjects')
>> recordings_dir =
>> op.expanduser('~/owncloud/Lab/Projects/SOLID_MEEG/data/HCPmeg')
>>
>> subjects =
>> glob.glob(op.join(storage_dir,'[0-9][0-9][0-9][0-9][0-9][0-9]'))
>>
>> src_fsaverage = mne.setup_source_space(
>>     subject='fsaverage',
>> subjects_dir='/network/lustre/iss01/cenir/software/meeg/freesurfer/subjects',
>> add_dist=False,
>>     spacing='oct6')
>>
>> for subject in subjects:
>>     hcp_params = dict(
>>         hcp_path=storage_dir,
>>         subject=subject,
>>         data_type='rest')
>>
>>     run_index = 0
>>
>>     hcp.make_mne_anatomy(
>>         subject, subjects_dir = subjects_dir,
>>         hcp_path = storage_dir,
>>         recordings_path = recordings_dir)
>>
>>     bems = mne.make_bem_model(subject, conductivity=(0.3,),
>>                               subjects_dir=subjects_dir,
>>                               ico=None)  # ico = None for morphed SP.
>>
>> mne.write_bem_surfaces(op.join(subjects_dir,subject,'bem',subject+'-bem.fif'),bems)
>>
>>     bem_sol = mne.make_bem_solution(bems)
>>     bem_sol['surfs'][0]['coord_frame'] = 5
>>
>>
>> mne.write_bem_solution(op.join(subjects_dir,subject,'bem',subject+'-bem-sol.fif'),bem_sol)
>>
>>     head_mri_t = mne.read_trans(
>>         op.join(recordings_dir, subject,
>> '{}-head_mri-trans.fif'.format(subject)))
>>
>>
>> mne.write_trans(op.join(subjects_dir,subject,'bem',subject+'-trans.fif'),head_mri_t)
>>
>>     info = hcp.read_info(run_index=run_index, **hcp_params)
>>     picks = mne.pick_types(info, meg=True, ref_meg=False)
>>     info = mne.pick_info(info, picks)
>>
>>
>> mne.viz.plot_alignment(info,head_mri_t,subject=subject,subjects_dir=subjects_dir,surfaces=('inner_skull','white'))
>>
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