PaCER preprocessing error in LeadDBS

[ariannafelice]

Dear all,
i'm trying to recostruct electrode trajectory using PaCER inside the toolbox matlab Lead-DBS and I got this error:

Warning: PaCER failed with the following error:
In ea_autocoord (line 270)
In ea_run (line 96)
In lead_dbs>run_button_Callback (line 187)
In gui_mainfcn (line 95)
In lead_dbs (line 43)
In matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)lead_dbs('run_button_Callback',hObject,eventdata,guidata(hObject))
Identifier:
Message: PaCER returned a different number of electrodes than expected by LeadDBS! In most cases this indicates an error in PaCER preprocessing (brain mask estimation) due to untypical CT data. Please provide a brain mask to PaCER in this case using the mask parameter.
In: C:\Users\BIOING\Desktop\STUDI\lead\ea_runpacer.m
Method: ea_runpacer
Line: 17
Please check your input data carefully.
Error using ea_reconstruct_trajectory (line 282)
Mask out of bounds! Must have lost trajectory...
Please try a different 'Mask window size' or try manual mode by setting 'Entrypoint for Target' to
'Manual'.
Error while evaluating UIControl Callback.

So i tried to run the "standalone use" of PaCER using my postop_CT images (.nii) and i got this error:

Error using extractElectrodePointclouds (line 96)
NO electrode artifact found within brain mask. Did you supply a post-op brain CT image? \n Try the 'no
mask' parameter in case of phantom scans without brain. \n Try providing an externally created brain
mask using the "brainMask" parameter in other cases.
Error in extractElectrodePointclouds (line 92)
[elecsPointcloudStruct, brainMask] = extractElectrodePointclouds(niiCT, 'brainMask',
args.brainMask, 'metalThreshold', METAL_THRESHOLD * 0.8, 'medtronicXMLPlan',
args.medtronicXMLPlan);
Error in extractElectrodePointclouds (line 92)
[elecsPointcloudStruct, brainMask] = extractElectrodePointclouds(niiCT, 'brainMask',
args.brainMask, 'metalThreshold', METAL_THRESHOLD * 0.8, 'medtronicXMLPlan',
args.medtronicXMLPlan);
Error in extractElectrodePointclouds (line 92)
[elecsPointcloudStruct, brainMask] = extractElectrodePointclouds(niiCT, 'brainMask',
args.brainMask, 'metalThreshold', METAL_THRESHOLD * 0.8, 'medtronicXMLPlan',
args.medtronicXMLPlan);
Error in extractElectrodePointclouds (line 92)
[elecsPointcloudStruct, brainMask] = extractElectrodePointclouds(niiCT, 'brainMask',
args.brainMask, 'metalThreshold', METAL_THRESHOLD * 0.8, 'medtronicXMLPlan',
args.medtronicXMLPlan);
Error in extractElectrodePointclouds (line 92)
[elecsPointcloudStruct, brainMask] = extractElectrodePointclouds(niiCT, 'brainMask',
args.brainMask, 'metalThreshold', METAL_THRESHOLD * 0.8, 'medtronicXMLPlan',
args.medtronicXMLPlan);
Error in extractElectrodePointclouds (line 92)
[elecsPointcloudStruct, brainMask] = extractElectrodePointclouds(niiCT, 'brainMask',
args.brainMask, 'metalThreshold', METAL_THRESHOLD * 0.8, 'medtronicXMLPlan',
args.medtronicXMLPlan);
Error in extractElectrodePointclouds (line 92)
[elecsPointcloudStruct, brainMask] = extractElectrodePointclouds(niiCT, 'brainMask',
args.brainMask, 'metalThreshold', METAL_THRESHOLD * 0.8, 'medtronicXMLPlan',
args.medtronicXMLPlan);
Error in extractElectrodePointclouds (line 92)
[elecsPointcloudStruct, brainMask] = extractElectrodePointclouds(niiCT, 'brainMask',
args.brainMask, 'metalThreshold', METAL_THRESHOLD * 0.8, 'medtronicXMLPlan',
args.medtronicXMLPlan);
Error in PaCER (line 51)
elecPointCloudsStruct = extractElectrodePointclouds(niiCT, varargin{:}); % preprocessing

Can somebody help me? Can someone give me some explanations?
Thanks in advace for your collaboration.
Regards,
Arianna

[andreashorn]

Hi Arianna,

we added a new function to PaCER in Lead-DBS that will automatically generate a brainmask from MNI. So maybe you can update to the newest git head (or run Install -> Install Developer Version) and rerun pacer?

Best, Andy

[ariannafelice]

Hi Andy,
I install developer version, but now i got this error:

Warning: Transformation contains off-diagnonal elements. Check carefully and consider reordering of data

In NiftiModSPM (line 64)
In ea_runpacer (line 10)
In ea_autocoord (line 273)
In ea_run (line 96)
In lead_dbs>run_button_Callback (line 187)
In gui_mainfcn (line 95)
In lead_dbs (line 43)
In @(hObject,eventdata)lead_dbs('run_button_Callback',hObject,eventdata,guidata(hObject))
Warning: PaCER failed with the following error:
In ea_autocoord (line 276)
In ea_run (line 96)
In lead_dbs>run_button_Callback (line 187)
In gui_mainfcn (line 95)
In lead_dbs (line 43)
In @(hObject,eventdata)lead_dbs('run_button_Callback',hObject,eventdata,guidata(hObject))
Identifier: MATLAB:cellRefFromNonCell
Message: Cell contents reference from a non-cell array object.
In: C:\Users\azzo\Desktop\lead\ea_apply_normalization_tofile.m
Method: ea_apply_normalization_tofile
Line: 62
Please check your input data carefully.
If the error persists, please consider a bug report at https://github.com/adhusch/PaCER/issues.
Error using ea_error (line 16)
PaCER failed. Potentially try running the TRAC/CORE Algorithm or a fully manual pre-reconstruction.

Error in ea_autocoord (line 284)
ea_error('PaCER failed. Potentially try running the TRAC/CORE Algorithm or a fully manual
pre-reconstruction.');

Error in ea_run (line 96)
ea_autocoord(options);

Error in lead_dbs>run_button_Callback (line 187)
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 @(hObject,eventdata)lead_dbs('run_button_Callback',hObject,eventdata,guidata(hObject))

Error while evaluating UIControl Callback

What's wrong?
Thanks.
Regards, Arianna

[adhusch]

Hi Arianna,

which normalisation options did you use? SPM based?

@andreashorn interesting that it fails now in
Method: ea_apply_normalization_tofile
Line: 62

Best
Andreas

[ariannafelice]

Hi Andreas,
generally, I use FSL FNIRT for the normalization. I tried to use SPM but the normalization was not very accurate. Instead, the default algorithm (ANTs) fails.

Thanks.
Regards, Arianna

[adhusch]

@ariannafelice could you provide an anonymized example dataset?