Error at localize electrode placement step

[cloz]

We are trying to run lead dbs on T1 MRI images. We are able to get through steps 1-5 fine. Our Coregister and normalization settings are: ANTs and Advanced Normalization Tools (Avants 2008). We are able to check the normalization and see that both the pre and post-op images are good. However, when we get to the step where we localize the DBS electrodes, a black blank window comes up and MATLAB displays the error below. Interestingly, we have been able to get this step to work if we use SPM SHOOT nonlinear (Ashburner 2011). We suspect that this is a problem with ANTs. Does anyone have any ideas what the problem could be? Thanks!

Calculating cross-correlation series for all x and y values within the cuboid volume.
Maximal value was: 6699829.1648.
/scratch/lead/ext_libs/ANTs/antsApplyTransformsToPoints.glnxa64: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20′ not found (required by /scratch/lead/ext_libs/ANTs/antsApplyTransformsToPoints.glnxa64)
/scratch/lead/ext_libs/ANTs/antsApplyTransformsToPoints.glnxa64: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21′ not found (required by /scratch/lead/ext_libs/ANTs/antsApplyTransformsToPoints.glnxa64)
Error using textscan
Invalid file identifier. Use fopen to generate a valid file identifier.

Error in ea_ants_applytransforms_to_points>ea_readcsv (line 91)
C=textscan(fid,’%f %f %f %f’,’commentStyle’, ‘#’,’delimiter’, ‘,’,’Headerlines’,1);

Error in ea_ants_applytransforms_to_points (line 84)
output=ea_readcsv([directory,’tmpout_’,guid,’.csv’]);

Error in ea_map_coords (line 333)
XYZ_dest_mm=ea_ants_applytransforms_to_points(directory,XYZ_src_mm(1:3,:)’,useinverse)’;

Error in ea_reconstruction2native>ea_warpcoord (line 78)
c=ea_map_coords(c(1:3,:), nii(1).fname,
[options.root,options.patientname,filesep,’y_ea_normparams.nii’],…

Error in ea_reconstruction2native (line 36)
reco.(usenative).coords_mm{side}=ea_warpcoord(reco.mni.coords_mm{side},nii,options);

Error in ea_load_reconstruction (line 18)
ea_reconstruction2native(options);

Error in ea_manualreconstruction (line 38)
[coords_mm,trajectory,markers,elmodel,manually_corrected]=ea_load_reconstruction(options);

Error in ea_autocoord (line 227)
ea_manualreconstruction(mcfig,options.patientname,options);

Error in ea_run (line 95)
ea_autocoord(options);

Error in lead_dbs>run_button_Callback (line 201)
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

[ningfei]

Hi, please check if you have this file /scratch/lead/ext_libs/support/libstdc++.so.6 (md5: b6532193067692c716a81da2194d733e). It should work if the newer lib file is at present. It will be loaded from lead folder first rather than use the system’s old one. If it still doesn’t work, you may try to add this line in your env or .bashrc: export LD_LIBRARY_PATH=/scratch/lead/ext_libs/support:$LD_LIBRARY_PATH to see if it works.

[cloz]

Hi ningrei, thanks for the reply. I’ll try your solution out on Monday and see if it works

[Author]

Posts