[Mne_analysis] [python read_inverse_operator()] Can not find parent MRI location

[Alexandre Gramfort]

hi Will,

I am not sure of what goes wrong on your side.

Can try the python script on the data available at:

ftp://surfer.nmr.mgh.harvard.edu/pub/data/MNE-sample-data-processed.tar.gz

it contains the processed dataset as obtained with the shell scripts
available on line and
the nightly build of MNE.

you can explore the content of a fif file with something like:

mne_show_fiff --in sample_audvis-meg-vol-7-meg-inv.fif

if the python script works with these files I suspect you have an
outdated version of MNE commands.

hope this helps,
Alex



On Tue, May 1, 2012 at 11:50 PM, Will Foran <willforan+mne at gmail.com> wrote:
> With help and a new mne_volume_source_space binary from Junpeng Zhang,
>  run_meg_volume_tutorial.sh finishes and produces the desired files,
> namely sample_audvis-meg-vol-7-meg-inv.fif.
>
> Now plot_compute_mne_inverse_volume.py fails with  "Can not find parent MRI
> location."  This error is raised by read_inverse_operator()
> reading sample_audvis-meg-vol-7-meg-inv.fif .
>
>
> I haven't had much success diving into the code, but from what I gather the
> fiff file(?) as explored by fiff/tree.py and fiff/tag.py does not include
> the tag for the parent MRI (FIFFB_MNE_PARENT_MRI_FILE=353).
>
>
> Is there a way to confirm this?
> Can a fiff file be easily modified to include it or is there a way to get
> python to look in a default location (
> environ['SUBJECT_DIR']/environ['SUBJECT']/MRI/ )?
>
>
> Thanks!
> Will
>
> ------------------------------------------
>
>
>
>>>> fname_inv
> '../MNE-sample-data/MEG/sample/sample_audvis-meg-vol-7-meg-inv.fif'
>
>>>> inverse_operator = read_inverse_operator(fname_inv)
>
> Reading inverse operator decomposition from
> ../MNE-sample-data/MEG/sample/sample_audvis-meg-vol-7-meg-inv.fif...
>     Reading inverse operator info... [done]
>     Reading inverse operator decomposition... [done]
>     305 x 305 full covariance (kind = 1) found.
>     Read a total of 4 projection items:
>         PCA-v1 (1 x 102) active
>         PCA-v2 (1 x 102) active
>         PCA-v3 (1 x 102) active
>         Average EEG reference (1 x 60) active
>     Noise covariance matrix read.
>     11271 x 11271 diagonal covariance (kind = 2) found.
>     Source covariance matrix read.
> Did not find the desired covariance matrix
>     11271 x 11271 diagonal covariance (kind = 5) found.
>     Depth priors read.
> Did not find the desired covariance matrix
>
> <open file
> '../MNE-sample-data/MEG/sample/sample_audvis-meg-vol-7-meg-inv.fif', mode
> 'rb' at 0x9bbfc80>
> ---------------------------------------------------------------------------
> ValueError                                Traceback (most recent call last)
> /home/foranw/src/MNE-sample-data/<ipython-input-15-2bc8ebaf3112> in
> <module>()
> ----> 1 inverse_operator = read_inverse_operator(fname_inv)
>
> /usr/lib/python2.7/site-packages/mne/minimum_norm/inverse.pyc in
> read_inverse_operator(fname)
>     187     #
>
>     188
> --> 189     inv['src'] = read_source_spaces_from_tree(fid, tree,
> add_geom=False)
>     190
>     191     for s in inv['src']:
>
> /usr/lib/python2.7/site-packages/mne/source_space.py in
> read_source_spaces_from_tree(fid, tree, add_geom)
>      81     for s in spaces:
>      82         print '    Reading a source space...',
> ---> 83         this = _read_one_source_space(fid, s)
>      84         print '[done]'
>      85         if add_geom:
>
> /usr/lib/python2.7/site-packages/mne/source_space.py in
> _read_one_source_space(fid, this)
>     153         parent_mri = dir_tree_find(this,
> FIFF.FIFFB_MNE_PARENT_MRI_FILE)
>     154         if len(parent_mri) == 0:
> --> 155             raise ValueError('Can not find parent MRI location')
>     156
>     157         mri = parent_mri[0]
>
> ValueError: Can not find parent MRI location
>
> ############
>
> $ grep -Ri 'FIFFB_MNE_PARENT_MRI_FILE.*='
> /usr/lib/python2.7/site-packages/mne
> /usr/lib/python2.7/site-packages/mne/fiff/constants.py:FIFF.FIFFB_MNE_PARENT_MRI_FILE
>    = 353
>
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