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Subject:

Re: Errors with SPM modelestimate

From:

Guillaume Flandin <[log in to unmask]>

Reply-To:

Guillaume Flandin <[log in to unmask]>

Date:

Fri, 18 Nov 2016 10:13:45 +0000

Content-Type:

multipart/mixed

Parts/Attachments:

Parts/Attachments

text/plain (318 lines) , spm_est_non_sphericity.m (291 lines)

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

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