[Mne_analysis] [python read_inverse_operator()] Can not find parent MRI location
Will Foran
willforan+mne at gmail.com
Tue May 1 17:50:02 EDT 2012
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<http://www.martinos.org/mne/auto_examples/inverse/plot_compute_mne_inverse_volume.html>
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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