[Mne_analysis] [python read_inverse_operator()] Can not find parent MRI location
Jon Houck
jhouck at unm.edu
Wed May 16 13:18:22 EDT 2012
Hi Alex,
The sample data has transforms for both MRI (surface RAS) -> head and MRI
(surface RAS) -> RAS (non-zero origin); my file had only MRI (surface RAS)
-> head. Re-running the MRI processing steps using 2.7.4 (from
mne_setup_source_space onward) added this tranformation, and a
slightly-modified version of the sample code gives me reasonable output in
volume source space. Thanks!
Jon
On Fri, May 11, 2012 at 11:14 AM, Alexandre Gramfort <
gramfort at nmr.mgh.harvard.edu> wrote:
> hi Jon,
>
> that's weird. I don't really have a clue.
>
> to inspect the content of the generated forward operator you can do
> something like this:
>
> mne_show_fiff --in sample_audvis-meg-vol-7-fwd.fif --verbose
>
> to only search for the coordinate transformation:
>
> mne_show_fiff --in sample_audvis-meg-vol-7-fwd.fif --verbose --tag 222
>
> you can then check the difference between the sample subject and yours
> and see if the transform is present or not in the fif file.
>
> Alex
>
> On Fri, May 11, 2012 at 3:08 PM, Jon Houck <jhouck at unm.edu> wrote:
> > I had the same problem using 2.7.3-3268 and mne-python v 0.3-1 with my
> data,
> > although it worked fine with the sample dataset.
> >
> > After switching to 2.7.4-3357, the sample dataset still works, but with
> my
> > own data now I get an error about the MRI RAS transformation matrix:
> > File
> >
> "/na/homes/jhouck/.local/lib/python2.6/site-packages/mne-0.3-py2.6.egg/mne/source_estimate.py",
> > line 799, in save_stc_as_volume
> > affine = np.dot(src[0]['mri_ras_t']['trans'], affine)
> > KeyError: 'mri_ras_t'
> >
> > I checked with mne_collect_transforms and this transform was present in
> all
> > of the MRI sets for my subject, as well as in talairach.xfm, but not in
> > T1.mgz. I applied it to that file using mri_add_xform_to_header but still
> > see the same error. Does that transfomation matrix need to exist in
> T1.mgz
> > before the source space and inverse solution are made?
> >
> > Thanks,
> >
> > Jon
> >
> >
> >
> >
> > On Wed, May 2, 2012 at 6:10 AM, Alexandre Gramfort
> > <gramfort at nmr.mgh.harvard.edu> wrote:
> >>
> >> 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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