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Dear Junhao,

What you found is a bug in the latest version of SPM12 (r6906) regarding
explicit masks in GLM estimation. Please copy the attached file in your
SPM installation and hopefully everything will run successfully thereafter.

Best regards,
Guillaume.


On 17/11/16 22:18, Junhao WEN wrote:
> Hello, SPM experts:
> 
> I am new to SPM, recently, I use this tutorial (nipype) to do 1st level
> analysis for
> fMRI: http://miykael.github.io/nipype-beginner-s-guide/firstLevel.html#visualize-your-pipeline
> 
> 
> But, I got some error from spm.modelestimate node, here is the
> information for the crash file:
> 
> 
> /File:
> crash-20161115-223547-junhao.wen-level1estimate.a3-2c105720-5e72-4cd8-a2fd-ccdebabb80f2.pklz/
> /Node: metaflow.l1analysis.level1estimate.a3/
> /Working directory:
> /Users/junhao.wen/Hao/tutorial/Nipype/Michael_Notter/nipype_tutorial/workingdir_fMRI_example_1st_level/metaflow/l1analysis/_subject_id_sub004/level1estimate/
> /
> /
> /
> /
> /Node inputs:/
> /
> /
> /estimation_method = {'Classical': 1}/
> /flags = <undefined>/
> /ignore_exception = False/
> /matlab_cmd = <undefined>/
> /mfile = True/
> /paths = <undefined>/
> /spm_mat_file =
> /Users/junhao.wen/Hao/tutorial/Nipype/Michael_Notter/nipype_tutorial/workingdir_fMRI_example_1st_level/metaflow/l1analysis/_subject_id_sub004/level1design/SPM.mat/
> /use_mcr = <undefined>/
> /use_v8struct = True/
> /
> /
> /
> /
> /
> /
> /Traceback:/
> /Traceback (most recent call last):/
> /  File
> "/Users/junhao.wen/anaconda/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py",
> line 49, in run_node/
> /    result['result'] = node.run(updatehash=updatehash)/
> /  File
> "/Users/junhao.wen/anaconda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py",
> line 394, in run/
> /    self._run_interface()/
> /  File
> "/Users/junhao.wen/anaconda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py",
> line 504, in _run_interface/
> /    self._result = self._run_command(execute)/
> /  File
> "/Users/junhao.wen/anaconda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py",
> line 630, in _run_command/
> /    result = self._interface.run()/
> /  File
> "/Users/junhao.wen/anaconda/lib/python2.7/site-packages/nipype/interfaces/base.py",
> line 1043, in run/
> /    runtime = self._run_wrapper(runtime)/
> /  File
> "/Users/junhao.wen/anaconda/lib/python2.7/site-packages/nipype/interfaces/base.py",
> line 1000, in _run_wrapper/
> /    runtime = self._run_interface(runtime)/
> /  File
> "/Users/junhao.wen/anaconda/lib/python2.7/site-packages/nipype/interfaces/spm/base.py",
> line 311, in _run_interface/
> /    results = self.mlab.run()/
> /  File
> "/Users/junhao.wen/anaconda/lib/python2.7/site-packages/nipype/interfaces/base.py",
> line 1043, in run/
> /    runtime = self._run_wrapper(runtime)/
> /  File
> "/Users/junhao.wen/anaconda/lib/python2.7/site-packages/nipype/interfaces/base.py",
> line 1660, in _run_wrapper/
> /    runtime = self._run_interface(runtime)/
> /  File
> "/Users/junhao.wen/anaconda/lib/python2.7/site-packages/nipype/interfaces/matlab.py",
> line 149, in _run_interface/
> /    self.raise_exception(runtime)/
> /  File
> "/Users/junhao.wen/anaconda/lib/python2.7/site-packages/nipype/interfaces/base.py",
> line 1618, in raise_exception/
> /    raise RuntimeError(message)/
> /RuntimeError: Command:/
> /matlab -nodesktop -nosplash -nodesktop -nosplash -singleCompThread -r
> "addpath('/Users/junhao.wen/Hao/tutorial/Nipype/Michael_Notter/nipype_tutorial/workingdir_fMRI_example_1st_level/metaflow/l1analysis/_subject_id_sub004/level1estimate');pyscript_estimatemodel;exit"/
> /Standard output:/
> /
> /
> /                            < M A T L A B (R) >/
> /                  Copyright 1984-2016 The MathWorks, Inc./
> /                   R2016a (9.0.0.341360) 64-bit (maci64)/
> /                             February 11, 2016/
> /
> /
> /
> /
> /To get started, type one of these: helpwin, helpdesk, or demo./
> /For product information, visit www.mathworks.com./
> /
> /
> /
> /
> /Academic License/
> /
> /
> /Executing pyscript_estimatemodel at 15-Nov-2016 22:35:22:/
> /----------------------------------------------------------------------------------------------------/
> /MATLAB Version: 9.0.0.341360 (R2016a)/
> /MATLAB License Number: 993575/
> /Operating System: Mac OS X  Version: 10.11.6 Build: 15G31/
> /Java Version: Java 1.7.0_75-b13 with Oracle Corporation Java
> HotSpot(TM) 64-Bit Server VM mixed mode/
> /----------------------------------------------------------------------------------------------------/
> /MATLAB                                                Version 9.0      
>   (R2016a)/
> /Simulink                                              Version 8.7      
>   (R2016a)/
> /Aerospace Toolbox                                     Version 2.17    
>    (R2016a)/
> /Bioinformatics Toolbox                                Version 4.6      
>   (R2016a)/
> /Communications System Toolbox                         Version 6.2      
>   (R2016a)/
> /Computer Vision System Toolbox                        Version 7.1      
>   (R2016a)/
> /Control System Toolbox                                Version 10.0    
>    (R2016a)/
> /Curve Fitting Toolbox                                 Version 3.5.3    
>   (R2016a)/
> /DSP System Toolbox                                    Version 9.2      
>   (R2016a)/
> /Database Toolbox                                      Version 6.1      
>   (R2016a)/
> /Econometrics Toolbox                                  Version 3.4      
>   (R2016a)/
> /Embedded Coder                                        Version 6.10    
>    (R2016a)/
> /Filter Design HDL Coder                               Version 3.0      
>   (R2016a)/
> /Financial Instruments Toolbox                         Version 2.3      
>   (R2016a)/
> /Financial Toolbox                                     Version 5.7      
>   (R2016a)/
> /Fixed-Point Designer                                  Version 5.2      
>   (R2016a)/
> /Fuzzy Logic Toolbox                                   Version 2.2.23  
>    (R2016a)/
> /Global Optimization Toolbox                           Version 3.4      
>   (R2016a)/
> /HDL Coder                                             Version 3.8      
>   (R2016a)/
> /Image Acquisition Toolbox                             Version 5.0      
>   (R2016a)/
> /Image Processing Toolbox                              Version 9.4      
>   (R2016a)/
> /Instrument Control Toolbox                            Version 3.9      
>   (R2016a)/
> /LTE System Toolbox                                    Version 2.2      
>   (R2016a)/
> /MATLAB Coder                                          Version 3.1      
>   (R2016a)/
> /MATLAB Compiler                                       Version 6.2      
>   (R2016a)/
> /MATLAB Compiler SDK                                   Version 6.2      
>   (R2016a)/
> /Mapping Toolbox                                       Version 4.3      
>   (R2016a)/
> /Model Predictive Control Toolbox                      Version 5.2      
>   (R2016a)/
> /Neural Network Toolbox                                Version 9.0      
>   (R2016a)/
> /Optimization Toolbox                                  Version 7.4      
>   (R2016a)/
> /Parallel Computing Toolbox                            Version 6.8      
>   (R2016a)/
> /Partial Differential Equation Toolbox                 Version 2.2      
>   (R2016a)/
> /RF Toolbox                                            Version 3.0      
>   (R2016a)/
> /Robotics System Toolbox                               Version 1.2      
>   (R2016a)/
> /Robust Control Toolbox                                Version 6.1      
>   (R2016a)/
> /Signal Processing Toolbox                             Version 7.2      
>   (R2016a)/
> /SimBiology                                            Version 5.4      
>   (R2016a)/
> /SimRF                                                 Version 5.0      
>   (R2016a)/
> /Simscape                                              Version 4.0      
>   (R2016a)/
> /Simscape Driveline                                    Version 2.10    
>    (R2016a)/
> /Simscape Electronics                                  Version 2.9      
>   (R2016a)/
> /Simscape Fluids                                       Version 2.0      
>   (R2016a)/
> /Simscape Multibody                                    Version 4.8      
>   (R2016a)/
> /Simscape Power Systems                                Version 6.5      
>   (R2016a)/
> /Simulink 3D Animation                                 Version 7.5      
>   (R2016a)/
> /Simulink Coder                                        Version 8.10    
>    (R2016a)/
> /Simulink Control Design                               Version 4.3      
>   (R2016a)/
> /Simulink Design Optimization                          Version 3.0      
>   (R2016a)/
> /Simulink Desktop Real-Time                            Version 5.2      
>   (R2016a)/
> /Simulink Verification and Validation                  Version 3.11    
>    (R2016a)/
> /Stateflow                                             Version 8.7      
>   (R2016a)/
> /Statistical Parametric Mapping                        Version 6906    
>    (SPM12)/
> /Statistics and Machine Learning Toolbox               Version 10.2    
>    (R2016a)/
> /Symbolic Math Toolbox                                 Version 7.0      
>   (R2016a)/
> /System Identification Toolbox                         Version 9.4      
>   (R2016a)/
> /Wavelet Toolbox                                       Version 4.16    
>    (R2016a)/
> /SPM version: SPM12 Release: 6906/
> /SPM path: /Users/junhao.wen/Software/spm12/spm.m/
> /
> /
> /
> /
> /------------------------------------------------------------------------/
> /Running job #1/
> /------------------------------------------------------------------------/
> /Running 'Model estimation'/
> /
> /
> /SPM12: spm_spm (v6842)                             22:35:41 - 15/11/2016/
> /========================================================================/
> /
> /
> /SPM12: spm_est_non_sphericity (v6827)              22:35:43 - 15/11/2016/
> /========================================================================/
> /Failed  'Model estimation'/
> /Reference to non-existent field 'xVol'./
> /In file "/Users/junhao.wen/Software/spm12/spm_est_non_sphericity.m"
> (v6827), function "spm_est_non_sphericity" at line 105./
> /In file "/Users/junhao.wen/Software/spm12/spm_spm.m" (v6842), function
> "spm_spm" at line 431./
> /In file "/Users/junhao.wen/Software/spm12/config/spm_run_fmri_est.m"
> (v5809), function "spm_run_fmri_est" at line 33./
> /
> /
> /The following modules did not run:/
> /Failed: Model estimation/
> /
> /
> /
> /
> /Standard error:/
> /MATLAB code threw an exception:/
> /Job execution failed. The full log of this run can be found in MATLAB
> command window, starting with the lines (look for the line showing the
> exact #job as displayed in this error message)/
> /------------------/
> /Running job #1/
> /------------------/
> /
> /
> /File:/
> /Name:MATLABbatch system/
> /Line:0/
> /
> /
> /Return code: 0/
> /Interface MatlabCommand failed to run./
> /Interface EstimateModel failed to run./
> 
> I have struggled for this for a while, because I dont know too much
> about SPM, can you help me???
> 
> I run the same tutorial code for my Mac and Linux, Linux works
> perfectly, so I guess I must have some problem for my SPM configuration.
> 
> 
> Thanks in advance
> 
> 
> 
> *Junhao WEN
> *
> Institut du Cerveau et de la Moelle Épinière - ICM
> Équipe ARAMIS / Projet CLINICA
> Web: http://www.aramislab.fr <http://www.aramislab.fr/>
> Twitter: @AramisLabParis <https://twitter.com/AramisLabParis>

-- 
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG