PaCER preprocessing error in LeadDBS about pacer

[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?