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kschan0214 / sepia

Matlab GUI pipeline application for quantitative susceptibility mapping (QSM)
MIT License
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Error running xQSM #77

Open MHoch96 opened 6 months ago

MHoch96 commented 6 months ago

When I run xQSM as the dipole inversion step, I get the following error:

The following QSM algorithm will be used: xQSM Warning: Name is nonexistent or not a directory: /home/common/matlab/sepia/external/deepMRI/xQSM/matlab/eval

In path (line 109) In addpath (line 86) In Wrapper_QSM_xQSM (line 39) In QSMMacro (line 108) In SepiaIOWrapper (line 327) In sepiaIO (line 79) In sepia_config_56 (line 38) In run (line 91) In sepia>PushbuttonStart_Callback (line 353) Warning: Name is nonexistent or not a directory: /home/common/matlab/sepia/external/deepMRI/xQSM_data/checkpoints In path (line 109) In addpath (line 86) In Wrapper_QSM_xQSM (line 40) In QSMMacro (line 108) In SepiaIOWrapper (line 327) In sepiaIO (line 79) In sepia_config_56 (line 38) In run (line 91) In sepia>PushbuttonStart_Callback (line 353) There was an error! Please check the command window/error message file for more information. Unrecognized function or variable 'field'.

Error in Wrapper_QSM_xQSM (line 50) [localField, pos] = ZeroPadding(field, 8);

Error in QSMMacro (line 108) chi = feval(wrapper_QSM_function{k},localField,mask,matrixSize_new,voxelSize,algorParam, headerAndExtraData);

Error in SepiaIOWrapper (line 327) [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_56 (line 38) sepiaIO(input,output_basename,mask_filename,algorParam);

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

Error in sepia>PushbuttonStart_Callback (line 353) run(configFilename);

Error while evaluating UIControl Callback.

Do I need to install another toolbox to use this method?

kschan0214 commented 5 months ago

Hi, to be able to use xQSM, you will need the extra toolbox and data from them. You may find the instructions for setting up xQSM here: https://github.com/kschan0214/sepia/tree/master/addons/qsm/xQSM or here: https://sepia-documentation.readthedocs.io/en/latest/method/qsm/xQSM.html