[PhilipM]

Ah, checking directory has solved the problem. I had renamed my folders with the suffix “v2.0” as I am re-running previous analyses and Matlab was confused by the decimal point. Sorry for the confusion and thanks for your assistance.

[PhilipM]

Thank you, I must have overlooked the newsletter about the re-naming. Regardless, still having difficulties – here is the information:
K>> pfcell
pfcell =
{}
K>> options.prefs.prenii_searchstring
ans =
anat_*.nii

And just in case it helps – here is the pasted ea_assignpretra:

function [options, presentfiles] = ea_assignpretra(options)

directory = [options.root,options.patientname,filesep];

presfiles=dir([directory,options.prefs.prenii_searchstring]);
pfcell = {presfiles.name}’;

% order the anatomical images in accordance with ‘prefs.prenii_order’
prenii_order = cellfun(@(x) strrep(options.prefs.prenii_searchstring,’*’,x), options.prefs.prenii_order, ‘UniformOutput’, 0);
[~,idx] = ismember(prenii_order, pfcell);
presentfiles = pfcell([nonzeros(idx)’,setdiff(1:numel(pfcell),nonzeros(idx))]);

if isempty(presentfiles)
ea_error([‘No anatomy information found!\nPlease put either ‘, …
prenii_order{1},’, ‘,prenii_order{2},’ or ‘,prenii_order{3},’ into subject folder.’], …
‘Error’, dbstack);
end

% set prenii_unnormalized
options.prefs.prenii_unnormalized = presentfiles{1};

% determine primary template
if any(idx)
options.primarytemplate = options.prefs.prenii_order{find(idx,1)};
else % could happen if neither T2, T1 or PD is present but only custom sequences are being used
options.primarytemplate = ‘t2’; % default T2.
end

[PhilipM]

Thank you, I will wait for later releases to test again. Best wishes.

[PhilipM]

Thank you!

[PhilipM]

No problem Andy, if I was smart enough I would do it myself but alas I am a mere clinician. Hopefully sometime soon you will get an enormous grant that will help free up some time for you :) Cheers, Phil

[PhilipM]

Thanks Andy, much appreciated. I can also load the .nii volumes manually into Matlab and calculate overlapping voxels myself, which gets around the problem too.

Can I point out one other issue that got me confused for a short while?

The 2D display flips the L-R orientation such that contact 0-3 are actually on the RIGHT electrode and contacts 8-11 are on the LEFT electrode. This threw me a bit, as the Medtronic and Boston leads are generally coded the other way around. At least here in Australasia.

Cheers, Phil

[PhilipM]

Thanks Andreas,

Regenerating the Accolla atlas file worked for me.

Unfortunately I am still getting the same error with the “Correlation Between Regressors and Volume Intersections / Fibrecounts” even after adding the patients, adding stimulation intensities, setting group colours and adding regressors, then pressing “Prepare Stats”. The full error is:

Reference to non-existent field ‘ft’.

Error in lead_group>preparedataanalysis (line 1143)
for side=1:size(M.stats(pt).ea_stats.stimulation(usewhichstim).ft,2)

Error in lead_group>corrbutton_Callback (line 365)
stats=preparedataanalysis(handles);

Error in gui_mainfcn (line 95)
feval(varargin{:});

Error in lead_group (line 42)
gui_mainfcn(gui_State, varargin{:});

Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)lead_group(‘corrbutton_Callback’,hObject,eventdata,guidata(hObject))
Error using ea_showatlas (line 284)
Error while evaluating UIControl Callback

Processing Lead_DBS_003.

When I then try to extract the information from the .mat file (Lead_groupanalysis.mat – stats – ea_stats – stimulation – vat) there is a 2×4 structure available, but the fields AtlasIntersection and nAtlasIntersection are all [0,0,0] even though the VATs are certainly imposed upon the STN subdivisions.

Am I following the right steps?

Much appreciated.

[PhilipM]

Update: I appear to have resolved this by manually selecting a contour colour in the 2D Settings box! Thanks

[PhilipM]

Thank you very much for the prompt reply and fix. Lead_group is now loading without difficulty.

Unfortunately I’m now having issues writing to 2D visualisations in lead_dbs. I’m attempting to use the STN Subdivisions (Accolla 2014), in MNI space. The error message I receive is below, any guidance would be most appreciated.

********************************************************************
Error using plot
Color value must be a 3 element vector

Error in ea_add_overlay (line 164)
plot(cscale(1,:),cscale(2,:),’color’,options.d2.con_color);

Error in ea_writeplanes (line 167)
cuts=ea_add_overlay(boundboxmm,cuts,tracor,options);

Error in ea_write (line 26)
cuts=ea_writeplanes(options);

Error in ea_autocoord (line 218)
ea_write(options)

Error in ea_run (line 102)
ea_autocoord(options);

Error in lead_dbs>run_button_Callback (line 278)
ea_run(‘run’,options);

Error in gui_mainfcn (line 95)
feval(varargin{:});

Error in lead_dbs (line 43)
gui_mainfcn(gui_State, varargin{:});

Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)lead_dbs(‘run_button_Callback’,hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback

[Author]

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