[Mne_analysis] Using mne_annot2labels

supra at nmr.mgh.harvard.edu supra at nmr.mgh.harvard.edu
Tue Feb 17 21:01:05 EST 2009
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Hi folks,

    I am trying to convert freesurfer parcellation data into labels using
mne_annot2labels(Page 241 of Manual) command. The command ran, however
the
converted label files when opened in text editor showed a row of  4 zeros
next to each vertex (meaning it did not look like a typical label file
which has the 3 coordinates corresponding to the vertex). Any help on 
successful use of this command will be appreciated.

Our aim is to load these converted labels  using mne_analyze and also to
compute the lead field matrices for each of these labels using
mne_forward_solution script. My expectation was that converted labels
using this command could be viewed  in the same way as manually created
labels (described in 7.13.4 of manual). Is this correct?

I ran the command from the directory labels which had the
following files
lh.aparc.a2005s.annot  lh.test_aparc.annot    rh.aparc.annot
lh.aparc.annot         rh.aparc.a2005s.annot
The command was used after correctly setting the SUBJECTS_DIR and SUBJECT
env variables was
mne_annot2labels --parc aparc

Here is what it returned
***************************************************************************
mne_annot2labels version 1.3 compiled at Feb  6 2009 08:01:35

Reading
/autofs/space/shadowfax_001/users/patrickp/eeg_propofol/eeganes03/structural_mri/surf/lh.white...
Triangle file : created by asalazar on Tue Nov 18 12:54:46 2008 nvert =
142811 ntri = 285618
        Triangle and vertex normals and neighboring triangles...[done]
        Vertex neighbors...[done]
        Distances between neighboring vertices...[856854 distances done]
Reading
/autofs/space/shadowfax_001/users/patrickp/eeg_propofol/eeganes03/structural_mri/surf/rh.white...
Triangle file : created by asalazar on Tue Nov 18 14:11:21 2008 nvert =
145119 ntri = 290234
        Triangle and vertex normals and neighboring triangles...[done]
        Vertex neighbors...[done]
        Distances between neighboring vertices...[870702 distances done]

Read 142811 parcellation vertices from
/autofs/space/shadowfax_001/users/patrickp/eeg_propofol/eeganes03/structural_mri/label/lh.aparc.annot
Read 35 parcellation entries from
/autofs/space/shadowfax_001/users/patrickp/eeg_propofol/eeganes03/structural_mri/label/lh.aparc.annot
Read 145119 parcellation vertices from
/autofs/space/shadowfax_001/users/patrickp/eeg_propofol/eeganes03/structural_mri/label/rh.aparc.annot
Read 35 parcellation entries from
/autofs/space/shadowfax_001/users/patrickp/eeg_propofol/eeganes03/structural_mri/label/rh.aparc.annot
Vertex assignments done for 35 left-hemisphere parcellations.
Vertex assignments done for 35 right-hemisphere parcellations.
Wrote unknown-lh.label
Wrote bankssts-lh.label
Wrote caudalanteriorcingulate-lh.label
Wrote caudalmiddlefrontal-lh.label
Wrote corpuscallosum-lh.label
Wrote cuneus-lh.label
Wrote entorhinal-lh.label
Wrote fusiform-lh.label
Wrote inferiorparietal-lh.label
Wrote inferiortemporal-lh.label
Wrote isthmuscingulate-lh.label
Wrote lateraloccipital-lh.label
Wrote lateralorbitofrontal-lh.label
Wrote lingual-lh.label
Wrote medialorbitofrontal-lh.label
Wrote middletemporal-lh.label
Wrote parahippocampal-lh.label
Wrote paracentral-lh.label
Wrote parsopercularis-lh.label
Wrote parsorbitalis-lh.label
Wrote parstriangularis-lh.label
Wrote pericalcarine-lh.label
Wrote postcentral-lh.label
Wrote posteriorcingulate-lh.label
Wrote precentral-lh.label
Wrote precuneus-lh.label
Wrote rostralanteriorcingulate-lh.label
Wrote rostralmiddlefrontal-lh.label
Wrote superiorfrontal-lh.label
Wrote superiorparietal-lh.label
Wrote superiortemporal-lh.label
Wrote supramarginal-lh.label
Wrote frontalpole-lh.label
Wrote temporalpole-lh.label
Wrote transversetemporal-lh.label
Wrote unknown-rh.label
Wrote bankssts-rh.label
Wrote caudalanteriorcingulate-rh.label
Wrote caudalmiddlefrontal-rh.label
Wrote corpuscallosum-rh.label
Wrote cuneus-rh.label
Wrote entorhinal-rh.label
Wrote fusiform-rh.label
Wrote inferiorparietal-rh.label
Wrote inferiortemporal-rh.label
Wrote isthmuscingulate-rh.label
Wrote lateraloccipital-rh.label
Wrote lateralorbitofrontal-rh.label
Wrote lingual-rh.label
Wrote medialorbitofrontal-rh.label
Wrote middletemporal-rh.label
Wrote parahippocampal-rh.label
Wrote paracentral-rh.label
Wrote parsopercularis-rh.label
Wrote parsorbitalis-rh.label
Wrote parstriangularis-rh.label
Wrote pericalcarine-rh.label
Wrote postcentral-rh.label
Wrote posteriorcingulate-rh.label
Wrote precentral-rh.label
Wrote precuneus-rh.label
Wrote rostralanteriorcingulate-rh.label
Wrote rostralmiddlefrontal-rh.label
Wrote superiorfrontal-rh.label
Wrote superiorparietal-rh.label
Wrote superiortemporal-rh.label
Wrote supramarginal-rh.label
Wrote frontalpole-rh.label
Wrote temporalpole-rh.label
Wrote transversetemporal-rh.label
****************************************************************************
 I opend the file  medialorbitofrontal-rh.label and it looked like this
(all files looked liked this). It appears it didnt run properly.
# medialorbitofrontal
2882
108997 0 0 0 0
109006 0 0 0 0
109035 0 0 0 0
109036 0 0 0 0
109037 0 0 0 0
109038 0 0 0 0
109039 0 0 0 0
109050 0 0 0 0
109051 0 0 0 0
109821 0 0 0 0
109829 0 0 0 0
109865 0 0 0 0
109866 0 0 0 0
109867 0 0 0 0
109868 0 0 0 0
109881 0 0 0 0
109882 0 0 0 0
110670 0 0 0 0
110676 0 0 0 0
110684 0 0 0 0
110701 0 0 0 0









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