Profile for User: Martijn Beudel

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  • 01/12/2018 at 3:57 PM in reply to: Import x,y,z coordinates #4006
    Martijn Beudel
    Participant

    thanks, that did the job! I can now import the electrodes in MNI space.

    01/12/2018 at 2:05 PM in reply to: Import x,y,z coordinates #4002
    Martijn Beudel
    Participant

    Hi Ningfei & Andy,

    thanks once more for the update. The new 2.0.0.6 version looks good. Unfortunately it was not until this Friday afternoon that I could manage to implement your suggestions and it seems like we’re getting somewhere.

    I can upload the above file in the 2.0.0.6 version in step 1 (of the ‘normal’ Lead DBS (i.e. not connectome or anatomy) toolbox and do see two electrodes in 3D in which changing parameters (i.e. z-coordinate values) result in sensible changes in space. Is, however, seems that the folder

    Error using spm_vol>spm_vol_hdr (line 80)
    File “/Applications/MATLAB74/leaddbs-master/templates/space/MNI_ICBM_2009b_NLIN_ASYM/t1.nii” does not exist.

    is missing the t1.nii file, which seems to be neccesary for visualisation. Does this sound familiar?

    ps I’m running ML 17b, although my archiving is a little bit archaic

    bw

    Martijn

    01/05/2018 at 4:47 PM in reply to: Import x,y,z coordinates #3952
    Martijn Beudel
    Participant

    Hi Andy,

    Indeed we tried two of our patients with the original images and were able to produce sensible results. I now moved the ea_reconstruction.mat file to a blank folder and (tried to) load it up in step 1 (specifying patient, electrode model and imaging method) and (immediately) visualise it (step 7). Unfortunately, I got the same error:

    Undefined function or variable ‘coords_mm’.

    could it still be that

    reco.mni.markers.head =[10 10 10]
    reco.mni.markers.tail =[10 10 0]
    ea_reconstruction = {[reco.mni.markers.head], [reco.mni.markers.tail]}

    does not generate the proper ea_reconstruction.mat file?

    bw

    Martijn

    01/05/2018 at 3:54 PM in reply to: Import x,y,z coordinates #3950
    Martijn Beudel
    Participant

    Hi Andy,

    many thanks for your quick reply and good to hear that this approach works. When trying to generate the ea_reconstruction.mat file for one hemisphere I entered:

    reco.mni.markers.head =[10 10 10]
    reco.mni.markers.tail =[10 10 0]

    ea_reconstruction = {[reco.mni.markers.head], [reco.mni.markers.tail]}

    save ea_reconstruction

    however, I’m not sure whether this suffices. When specifying this file in section 1 (specifying patient, electrode model and imaging method) of leadDBS and choosing ‘ea_reconstruction’ in the second scroll down menu, the
    word ‘ea_reconstruction’ is immediately replaced with ‘Recent Recent patients’ . Furthermore, when running steps 5, (6) or 7 I get the following error:

    ** Process done.
    Invalid MEX-file ‘/Applications/MATLAB74/spm12/spm_existfile.mexmaci64’: dlopen(/Applications/MATLAB74/spm12/spm_existfile.mexmaci64, 6): Library not loaded:
    @loader_path/libmex.dylib
    Referenced from: /Applications/MATLAB74/spm12/spm_existfile.mexmaci64
    Reason: image not found.

    I presume this has to do with either the incorrect format of the ea_reconstruction.mat file or the wrong visualisation step.

    bw

    Martijn

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