[Mne_analysis] mne.save_stc_as_volume('lcmv_inverse.nii.gz', stc, fwd['src'], mri_resolution=False)

dgw dgwakeman at gmail.com
Wed Apr 13 23:33:59 EDT 2016
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Hi Parham,
Where are you getting src from? It doesn't seem to be a volume source space.

hth
d
Sent from my Phone

> On Apr 13, 2016, at 18:01, parham hashemzadeh <ph442 at cam.ac.uk> wrote:
> 
> Dear
>  Thank you for your email. But actually no I am not using that tutorial. 
> I am using this tutorial which is focused on the Volume Source Space.
> 
> http://martinos.org/mne/dev/auto_examples/inverse/plot_lcmv_beamformer_volume.html#sphx-glr-auto-examples-inverse-plot-lcmv-beamformer-volume-py
> 
> All I am doing is that I am turning off the MEG and just want to use the 
> EEG.
> 
> In theory it should work even with this reduced leadfield matrix. Before 
> it was 366 rows but now only 60 rows (Just EEG).
> 
> So my volume (source space) does not change. It is exactly the same 
> thing. My number of sensors are reduced.
> 
> The error happens at the line below:
> mne.save_stc_as_volume('lcmv_inverse.nii.gz', stc, fwd['src'], 
> mri_resolution=False)
> 
> ""Only volume source estimates can be saved as volumes"" can be saved
> 
> Any help will be appreciated.
> besst regards parham
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>> On 2016-04-13 21:41, dgw wrote:
>> Hi Parham,
>> 
>> It sounds like you are using this tutorial:
>> 
>> http://martinos.org/mne/dev/auto_examples/inverse/plot_lcmv_beamformer.html?highlight=beamformer
>> 
>> If that is the case, it uses the cortical surface as the source space
>> and not a volume, so it doesn't really make sense to save as a nifti.
>> 
>> hth
>> d
>> 
>> On Wed, Apr 13, 2016 at 3:48 PM, parham hashemzadeh <ph442 at cam.ac.uk> 
>> wrote:
>>> Dear all
>>> 
>>> I got an error when running a beamforming tutorial script. I modified
>>> the beamformer such that only the EEG leadfield is used and I just
>>> wanted to do EEG analysis.
>>> So I made the following changes:
>>> (a) meg=False in fwd
>>> (b) in epochs reject=dict(eog=150e-6)
>>> When it gets to the function lcm_inverse, it throws an error:
>>> 
>>> ""Only volume source estimates can be saved as volumes"" can be saved
>>> 
>>> 
>>> 
>>>  I was wondering, if you would be able to point me in the right
>>> direction.
>>> Many thanks
>>> best regards parham hashemzadeh
>>> 
>>> 
>>> 
>>> fwd = mne.make_forward_solution(raw_fname, trans, src, bem,
>>>                                 fname=None, meg=False, eeg=True,
>>> mindist=5.0,
>>>                                 n_jobs=2, overwrite=True)
>>> epochs = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True,
>>>                     picks=picks, baseline=(None, 0), preload=True,
>>>                     reject=dict(eog=150e-6))
>>> 
>>> evoked = epochs.average()
>>> leadfield = fwd['sol']['data']
>>> ## Read regularized noise covariance and compute regularized data
>>> covariance
>>> noise_cov = mne.read_cov(fname_cov)
>>> data_cov = mne.compute_covariance(epochs, tmin=0.04,
>>> tmax=0.15,method='shrunk')
>>> #
>>> ## Run free orientation (vector) beamformer. Source orientation can be
>>> ## restricted by setting pick_ori to 'max-power' (or 'normal' but only
>>> when
>>> ## using a surface-based source space)
>>> stc = lcmv(evoked, fwd, noise_cov, data_cov, reg=0.01, pick_ori=None)
>>> #
>>> ## Save result in stc files
>>> stc.save('lcmv-vol')
>>> stc.crop(0.0, 0.2)
>>> ## Save result in a 4D nifti file
>>> img = mne.save_stc_as_volume('lcmv_inverse.nii.gz',
>>> stc,fwd['src'],mri_resolution=False)
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> 
> -- 
> best regards
> Parham Hashemzadeh
> Research Associate
> Department of Applied Mathematics and Theoretical Physics
> University of Cambridge, UK.
> email: hashemzadeh at damtp.cam.ac.uk
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