CSF referencing raises error: index exceeds number of array elements

[fprinse]

Hi,

I'm running the SEPIA pipeline but in the dipole inversion step I get an error regarding index exceeding the number of array elements with using CSF as a reference tissue:

Index exceeds the number of array elements. Index must not exceed 1.

Error in extract_CSF (line 43)
numPixels_sorted(i);

Error in QSMMacro (line 92)
mask_ref = extract_CSF(r2s,mask,voxelSize)>0;

Error in SepiaIOWrapper (line 322)
[chi,mask_ref] = QSMMacro(localField,mask_QSM,matrixSize,voxelSize,algorParam,headerAndExtraData);

Error in sepiaIO (line 79)
SepiaIOWrapper(input,output,maskFullName,algorParam);

Error in sepia_config (line 38)
sepiaIO(input,output_basename,mask_filename,algorParam);

Error in run (line 91)
evalin('caller', strcat(script, ';'));

Error in sepia>PushbuttonStart_Callback (line 350)
run(configFilename);

Error while evaluating UIControl Callback.

I provided 4D phase and magnitude images acquired on a Siemens 7T. I combined the echoes using MATLAB. I haven't had this error previously using the same configuration

Thanks!

[kschan0214]

Hi, sorry for the late follow up! Have you been able to find a solution yet? It seems to me that something went wrong with the brain mask but I cannot be sure without checking the input data.