nipype can't find spm even though it on the matlab path

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Dylan Nielson

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Jul 20, 2013, 5:27:19 PM7/20/13
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I'm trying to run tutorial 1 and it reports that spm is not on the matlab path.

I'm pretty sure that spm is on the mathlab path, if I type which spm in matlab it returns /usr/share/spm8/spm.m.

I've attached the crash file.

Thanks,

Dylan
crash-20130720-172407-dylan-realign.npz

Satrajit Ghosh

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Jul 21, 2013, 9:39:06 AM7/21/13
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hi dylan,

could you please post the crashdump? you can simply do:

nipype_display_crash crash_file

also to test spm in the path, you can do:

```
In [1]: from nipype.interfaces.spm import Info

In [4]: Info.version()
Out[4]: {'name': 'SPM8', 'path': '/software/matlab/spm8', 'release': '5236'}
```

if this errors, then we have an issue with path existence.

finally, we will include this in the crashdump, but could you also please send us the following info:

python -c "import nipype; print nipype.get_info()"

cheers,

satra

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Ryan Sherrock

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Aug 5, 2013, 12:48:15 AM8/5/13
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I also have the same problem.  Here is the workflow
import nipype.interfaces.spm as spm
import nipype.pipeline.engine as pe

realigner = pe.Node(interface=spm.Realign(), name='realign')
realigner.inputs.in_files = "/home/dylan/fmri/nipype/nki_test/tutorial_data/nipype-tutorial/data/s1/struct.nii" #chane to data file
realigner.inputs.register_to_mean = True

smoother = pe.Node(interface=spm.Smooth(fwhm=6), name='smooth')
smoother.inputs.in_files = "/home/dylan/fmri/nipype/nki_test/tutorial_data/nipype-tutorial/data/s1/struct.nii"
"""
datasink = pe.Node(nio.DataSink(), name='sinker')
datasink.inputs.base_directory = '/home/dylan/fmri/nipype/nki_test/tutorial_data'
"""

workflow = pe.Workflow(name='preproc')
workflow.base_dir = '.'
workflow.add_nodes([smoother, realigner])
workflow.connect(realigner, 'realigned_files', smoother, 'in_files')
workflow.run()

This is in the error message.  I'm not sure if it helps but it seems important.
Standard error:
No window system found.  Java option 'MWT' ignored.
MATLAB code threw an exception:
SPM not in matlab path
File:/home/dylan/preproc/realign/pyscript_realign.m
Name:pyscript_realign
Line:6

This is the output for python -c "import nipype; print nipype.get_info()"

{'nibabel_version': '1.3.0', 'networkx_version': '1.6', 'numpy_version': '1.6.1', 'sys_platform': 'linux2', 'sys_version': '2.7.3 (default, Apr 10 2013, 06:20:15) \n[GCC 4.6.3]', 'commit_source': 'archive substitution', 'commit_hash': '9595f27', 'pkg_path': '/usr/lib/pymodules/python2.7/nipype', 'sys_executable': '/usr/bin/python', 'traits_version': '4.0.0', 'scipy_version': '0.9.0'}

and here is the crash file 
crash-20130805-033127-dylan-realign.npz

Satrajit Ghosh

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Aug 5, 2013, 9:14:41 AM8/5/13
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hi ryan and dylan,

to add matlab to the spm path within nipype you can do:

import nipype.interfaces.matlab as mlab
mlab.MatlabCommand.set_default_paths('/path/to/spm8')

this also helpful when you want to switch between versions of matlab across projects without changing your matlab defaults, or to add custom matlab paths.


however, i'm more concerned as to why matlab called from nipype won't pick up the default path. this might be due to some change in behavior in matlab. could you please let me know:

1. whether you had to set MATLABCMD as part of the install (http://nipy.org/nipype/users/install.html#testing-the-install)
2. which version of matlab you have (ver inside matlab will tell you)  
3. the output of `which matlab`
4. whether matlab is aliased in your environment `alias | grep matlab`

cheers,

satra

Ryan Sherrock

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Aug 8, 2013, 9:41:43 AM8/8/13
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I have added those lines to my pipeline and I still get the same error.  Is there something else that might work?

1. I'm having trouble running the test.  I am getting syntax errors even though I have copied and pasted straight from the page.  the code I am trying to use looks like this
python -c "import nipype; nipype.test()"
export MATLABCMD=$/home/dylan/bin/$glnxa64/MATLAB

2.MATLAB Version: 8.1.0.604 (R2013a)
3. /usr/bin/matlab
4.  that command didn't return anything in the terminal so I'm going to guess that it is not.  

Satrajit Ghosh

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Aug 13, 2013, 1:18:15 PM8/13/13
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hi ryan,

let's break this down a little further:

in your terminal do:

$ unset MATLABCMD
$ python -c "from nipype.interfaces.matlab import MatlabCommand; res = MatlabCommand(script='''path''', mfile=False).run(); print res.runtime.stdout"

if you have spm in your default path, it will show up here.

if not then in a python terminal do the following - replace fullpath_to_spm with your spm path. this will add spm to the path.

from nipype.interfaces.matlab import MatlabCommand
res = MatlabCommand(script='''which(spm)''', paths=[fullpath_to_spm], mfile=False).run()
print res.runtime.stdout

cheers,

satra

Ryan Sherrock

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Aug 15, 2013, 11:30:03 PM8/15/13
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The out put of that shows that SPM is in the path I do believe, but it still isnt working.

It is crashing on a realign node, and the error log says that it is looking in dir: /home/dylan/preproc/realign130802-17:32:20,487

Does this give us any clues as to what is going wrong?

Control System Toolbox                                Version 9.5        (R2013a)
Curve Fitting Toolbox                                 Version 3.3.1      (R2013a)
DSP System Toolbox                                    Version 8.4        (R2013a)
Fuzzy Logic Toolbox                                   Version 2.2.17     (R2013a)
Image Processing Toolbox                              Version 8.2        (R2013a)
Instrument Control Toolbox                            Version 3.3        (R2013a)
MATLAB Compiler                                       Version 4.18.1     (R2013a)
Neural Network Toolbox                                Version 8.0.1      (R2013a)
Optimization Toolbox                                  Version 6.3        (R2013a)
Parallel Computing Toolbox                            Version 6.2        (R2013a)
Partial Differential Equation Toolbox                 Version 1.2        (R2013a)
Robust Control Toolbox                                Version 4.3        (R2013a)
Signal Processing Toolbox                             Version 6.19       (R2013a)
SimMechanics                                          Version 4.2        (R2013a)
Simscape                                              Version 3.9        (R2013a)
Simulink Control Design                               Version 3.7        (R2013a)
Stateflow                                             Version 8.1        (R2013a)
Statistical Parametric Mapping                        Version 5236       (SPM8)  
Statistics Toolbox                                    Version 8.2        (R2013a)
Symbolic Math Toolbox                                 Version 5.10       (R2013a)
System Identification Toolbox                         Version 8.2        (R2013a)
Wavelet Toolbox                                       Version 4.11       (R2013a)

MATLABPATH

/home/dylan/Documents/MATLAB
/home/dylan/matlab
/home/dylan/host_dylan
/home/dylan/host_dylan/preproc
/home/dylan/host_dylan/preproc/realign
/home/dylan/host_dylan/preproc/realign/_report
/home/dylan/host_dylan/preproc/report
/home/dylan/host_dylan/matlab
/home/dylan/host_dylan/MATLAB
/home/dylan/host_dylan/MATLAB/art
/home/dylan/host_dylan/MATLAB/conn
/home/dylan/host_dylan/MATLAB/conn/conn
/home/dylan/host_dylan/MATLAB/conn/conn/rois
/home/dylan/host_dylan/MATLAB/conn/conn/utils
/home/dylan/host_dylan/MATLAB/conn/conn/utils/otherrois
/usr/share/spm8
/usr/share/spm8/EEGtemplates
/usr/share/spm8/apriori
/usr/share/spm8/canonical
/usr/share/spm8/config
/usr/share/spm8/man
/usr/share/spm8/man/images
/usr/share/spm8/matlabbatch
/usr/share/spm8/matlabbatch/cfg_basicio
/usr/share/spm8/matlabbatch/cfg_basicio/src
/usr/share/spm8/matlabbatch/cfg_confgui
/usr/share/spm8/matlabbatch/examples
/usr/share/spm8/rend
/usr/share/spm8/spm_orthviews
/usr/share/spm8/src
/usr/share/spm8/templates
/usr/share/spm8/toolbox
/usr/share/spm8/toolbox/Beamforming
/usr/share/spm8/toolbox/DARTEL
/usr/share/spm8/toolbox/DEM
/usr/share/spm8/toolbox/FieldMap
/usr/share/spm8/toolbox/HDW
/usr/share/spm8/toolbox/MEEGtools
/usr/share/spm8/toolbox/Neural_Models
/usr/share/spm8/toolbox/SRender
/usr/share/spm8/toolbox/Seg
/usr/share/spm8/toolbox/Shoot
/usr/share/spm8/toolbox/dcm_meeg
/usr/share/spm8/toolbox/mixture
/usr/share/spm8/toolbox/spectral
/usr/share/spm8/tpm
/usr/local/MATLAB/R2013a/toolbox/local
/usr/local/MATLAB/R2013a/toolbox/matlab/codetools
/usr/local/MATLAB/R2013a/toolbox/matlab/datafun
/usr/local/MATLAB/R2013a/toolbox/matlab/datamanager
/usr/local/MATLAB/R2013a/toolbox/matlab/datatypes
/usr/local/MATLAB/R2013a/toolbox/matlab/elfun
/usr/local/MATLAB/R2013a/toolbox/matlab/elmat
/usr/local/MATLAB/R2013a/toolbox/matlab/funfun
/usr/local/MATLAB/R2013a/toolbox/matlab/general
/usr/local/MATLAB/R2013a/toolbox/matlab/guide
/usr/local/MATLAB/R2013a/toolbox/matlab/helptools
/usr/local/MATLAB/R2013a/toolbox/matlab/iofun
/usr/local/MATLAB/R2013a/toolbox/matlab/lang
/usr/local/MATLAB/R2013a/toolbox/matlab/matfun
/usr/local/MATLAB/R2013a/toolbox/matlab/ops
/usr/local/MATLAB/R2013a/toolbox/matlab/polyfun
/usr/local/MATLAB/R2013a/toolbox/matlab/randfun
/usr/local/MATLAB/R2013a/toolbox/matlab/sparfun
/usr/local/MATLAB/R2013a/toolbox/matlab/specfun
/usr/local/MATLAB/R2013a/toolbox/matlab/strfun
/usr/local/MATLAB/R2013a/toolbox/matlab/timefun
/usr/local/MATLAB/R2013a/toolbox/matlab/verctrl
/usr/local/MATLAB/R2013a/toolbox/matlab/optimfun
/usr/local/MATLAB/R2013a/toolbox/matlab/demos
/usr/local/MATLAB/R2013a/toolbox/matlab/graph2d
/usr/local/MATLAB/R2013a/toolbox/matlab/graph3d
/usr/local/MATLAB/R2013a/toolbox/matlab/graphics
/usr/local/MATLAB/R2013a/toolbox/matlab/plottools
/usr/local/MATLAB/R2013a/toolbox/matlab/scribe
/usr/local/MATLAB/R2013a/toolbox/matlab/specgraph
/usr/local/MATLAB/R2013a/toolbox/matlab/uitools
/usr/local/MATLAB/R2013a/toolbox/matlab/testframework
/usr/local/MATLAB/R2013a/toolbox/simulink/simdemos/dataclasses
/usr/local/MATLAB/R2013a/toolbox/simulink/simdemos
/usr/local/MATLAB/R2013a/toolbox/shared/glue
/usr/local/MATLAB/R2013a/toolbox/shared/glue/studio
/usr/local/MATLAB/R2013a/toolbox/simulink/simulink/frameedit
/usr/local/MATLAB/R2013a/toolbox/simulink/blocks
/usr/local/MATLAB/R2013a/toolbox/simulink/fixedandfloat
/usr/local/MATLAB/R2013a/toolbox/simulink/fixedandfloat/obsolete
/usr/local/MATLAB/R2013a/toolbox/simulink/simulink/dataclasses
/usr/local/MATLAB/R2013a/toolbox/simulink/simulink
/usr/local/MATLAB/R2013a/toolbox/simulink/simulink/MPlayIO
/usr/local/MATLAB/R2013a/toolbox/simulink/simulink/dataobjectwizard
/usr/local/MATLAB/R2013a/toolbox/simulink/simulink/slresolve
/usr/local/MATLAB/R2013a/toolbox/simulink/simdemos/automotive
/usr/local/MATLAB/R2013a/toolbox/simulink/simulink/modeladvisor
/usr/local/MATLAB/R2013a/toolbox/simulink/simulink/modeladvisor/fixpt
/usr/local/MATLAB/R2013a/toolbox/simulink/simdemos/industrial
/usr/local/MATLAB/R2013a/toolbox/simulink/simdemos/simgeneral
/usr/local/MATLAB/R2013a/toolbox/simulink/blocks/library
/usr/local/MATLAB/R2013a/toolbox/simulink/blocks/obsolete
/usr/local/MATLAB/R2013a/toolbox/simulink/simdemos/aerospace
/usr/local/MATLAB/R2013a/toolbox/simulink/simdemos/simfeatures
/usr/local/MATLAB/R2013a/toolbox/rtw/targets/AUTOSAR/AUTOSAR/dataclasses
/usr/local/MATLAB/R2013a/toolbox/rtw/targets/AUTOSAR/AUTOSAR
/usr/local/MATLAB/R2013a/toolbox/rtw/accel
/usr/local/MATLAB/R2013a/toolbox/coder/simulinkcoder_core
/usr/local/MATLAB/R2013a/toolbox/simulink/simdemos/automotive/fuelsys
/usr/local/MATLAB/R2013a/toolbox/simulink/components
/usr/local/MATLAB/R2013a/toolbox/simulink/dee
/usr/local/MATLAB/R2013a/toolbox/stateflow/stateflow
/usr/local/MATLAB/R2013a/toolbox/stateflow/coder
/usr/local/MATLAB/R2013a/toolbox/stateflow/sfdemos
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/sli/m
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/ssci/m
/usr/local/MATLAB/R2013a/toolbox/slvnv/reqmgt
/usr/local/MATLAB/R2013a/toolbox/slvnv/reqmgt/RTExplorer
/usr/local/MATLAB/R2013a/toolbox/slvnv/slvnv
/usr/local/MATLAB/R2013a/toolbox/shared/cgxe/cgxe
/usr/local/MATLAB/R2013a/toolbox/simulink/simulink/slproject
/usr/local/MATLAB/R2013a/toolbox/physmod/common/data/mli/m
/usr/local/MATLAB/R2013a/toolbox/physmod/ne_sli/ne_sli
/usr/local/MATLAB/R2013a/toolbox/slcontrol/slctrldemos
/usr/local/MATLAB/R2013a/toolbox/coder/rtiostream
/usr/local/MATLAB/R2013a/toolbox/matlab/connector/connector
/usr/local/MATLAB/R2013a/toolbox/shared/system/coreblocks
/usr/local/MATLAB/R2013a/toolbox/nnet
/usr/local/MATLAB/R2013a/toolbox/nnet/nncontrol
/usr/local/MATLAB/R2013a/toolbox/nnet/nndemos
/usr/local/MATLAB/R2013a/toolbox/nnet/nndemos/nndatasets
/usr/local/MATLAB/R2013a/toolbox/nnet/nnet
/usr/local/MATLAB/R2013a/toolbox/nnet/nnet/nnadapt
/usr/local/MATLAB/R2013a/toolbox/nnet/nnet/nndatafun
/usr/local/MATLAB/R2013a/toolbox/nnet/nnet/nnderivative
/usr/local/MATLAB/R2013a/toolbox/nnet/nnet/nndistance
/usr/local/MATLAB/R2013a/toolbox/nnet/nnet/nndivision
/usr/local/MATLAB/R2013a/toolbox/nnet/nnet/nninitlayer
/usr/local/MATLAB/R2013a/toolbox/nnet/nnet/nninitnetwork
/usr/local/MATLAB/R2013a/toolbox/nnet/nnet/nninitweight
/usr/local/MATLAB/R2013a/toolbox/nnet/nnet/nnlearn
/usr/local/MATLAB/R2013a/toolbox/nnet/nnet/nnnetfun
/usr/local/MATLAB/R2013a/toolbox/nnet/nnet/nnnetinput
/usr/local/MATLAB/R2013a/toolbox/nnet/nnet/nnnetwork
/usr/local/MATLAB/R2013a/toolbox/nnet/nnet/nnperformance
/usr/local/MATLAB/R2013a/toolbox/nnet/nnet/nnplot
/usr/local/MATLAB/R2013a/toolbox/nnet/nnet/nnprocess
/usr/local/MATLAB/R2013a/toolbox/nnet/nnet/nnsearch
/usr/local/MATLAB/R2013a/toolbox/nnet/nnet/nntopology
/usr/local/MATLAB/R2013a/toolbox/nnet/nnet/nntrain
/usr/local/MATLAB/R2013a/toolbox/nnet/nnet/nntransfer
/usr/local/MATLAB/R2013a/toolbox/nnet/nnet/nnweight
/usr/local/MATLAB/R2013a/toolbox/nnet/nnguis
/usr/local/MATLAB/R2013a/toolbox/nnet/nnobsolete
/usr/local/MATLAB/R2013a/toolbox/nnet/nnutils
/usr/local/MATLAB/R2013a/toolbox/shared/configset
/usr/local/MATLAB/R2013a/toolbox/shared/statslib
/usr/local/MATLAB/R2013a/toolbox/shared/testmeaslib/graphics
/usr/local/MATLAB/R2013a/toolbox/shared/system/coder
/usr/local/MATLAB/R2013a/toolbox/sldv/sldv
/usr/local/MATLAB/R2013a/toolbox/shared/imageslib
/usr/local/MATLAB/R2013a/toolbox/physmod/simscape/simscapedemos
/usr/local/MATLAB/R2013a/toolbox/shared/siglib
/usr/local/MATLAB/R2013a/toolbox/sl3d/sl3d
/usr/local/MATLAB/R2013a/toolbox/shared/coder/coder
/usr/local/MATLAB/R2013a/toolbox/physmod/network_engine/ne_support
/usr/local/MATLAB/R2013a/toolbox/physmod/network_engine/network_engine
/usr/local/MATLAB/R2013a/toolbox/simulink/fixedandfloat/fxpdemos
/usr/local/MATLAB/R2013a/toolbox/stats/statsdemos
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/images
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/wing_landing_gear
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/wing_landing_gear/images
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/cart_double_pendulum
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/cart_double_pendulum/images
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/stewart_platform
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/stewart_platform/images
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/double_crank_aiming
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/double_crank_aiming/images
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/bread_slicer
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/bread_slicer/images
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/import/stewart_platform
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/import/four_bar
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/radial_engine
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/radial_engine/images
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/double_wishbone_suspension
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/double_wishbone_suspension/images
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/import/robot
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/cardan_gear
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/cardan_gear/images
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/windshield_wiper
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/windshield_wiper/images
/usr/local/MATLAB/R2013a/toolbox/physmod/sm/smdemos/backhoe
/usr/local/MATLAB/R2013a/toolbox/shared/testmeaslib/simulink
/usr/local/MATLAB/R2013a/toolbox/shared/instrument
/usr/local/MATLAB/R2013a/toolbox/ident/ident
/usr/local/MATLAB/R2013a/toolbox/ident/nlident
/usr/local/MATLAB/R2013a/toolbox/ident/idobsolete
/usr/local/MATLAB/R2013a/toolbox/ident/idguis
/usr/local/MATLAB/R2013a/toolbox/ident/idutils
/usr/local/MATLAB/R2013a/toolbox/ident/idhelp
/usr/local/MATLAB/R2013a/toolbox/compiler/compilerdemos
/usr/local/MATLAB/R2013a/toolbox/shared/dspblks/dspblks
/usr/local/MATLAB/R2013a/toolbox/shared/dspblks/dspmex
/usr/local/MATLAB/R2013a/toolbox/physmod/equation_language/equation_language
/usr/local/MATLAB/R2013a/toolbox/physmod/simscape/compiler/core/m
/usr/local/MATLAB/R2013a/toolbox/simulink/blocks/sb2sl
/usr/local/MATLAB/R2013a/toolbox/shared/dsp/hdl
/usr/local/MATLAB/R2013a/toolbox/shared/system/sfun
/usr/local/MATLAB/R2013a/toolbox/physmod/simscape/foundation/simscape
/usr/local/MATLAB/R2013a/toolbox/slcontrol/slcontrol
/usr/local/MATLAB/R2013a/toolbox/slcontrol/slctrlguis
/usr/local/MATLAB/R2013a/toolbox/slcontrol/slctrlutil
/usr/local/MATLAB/R2013a/toolbox/slcontrol/slctrlobsolete
/usr/local/MATLAB/R2013a/toolbox/matlab/apps
/usr/local/MATLAB/R2013a/toolbox/stm/stm
/usr/local/MATLAB/R2013a/toolbox/images/imdemos
/usr/local/MATLAB/R2013a/toolbox/shared/sigbldr
/usr/local/MATLAB/R2013a/toolbox/shared/comparisons
/usr/local/MATLAB/R2013a/toolbox/optim/optimdemos
/usr/local/MATLAB/R2013a/toolbox/matlab/timeseries
/usr/local/MATLAB/R2013a/toolbox/matlab/hds
/usr/local/MATLAB/R2013a/toolbox/stm/stmdemos
/usr/local/MATLAB/R2013a/toolbox/shared/asynciolib
/usr/local/MATLAB/R2013a/toolbox/curvefit/curvefit
/usr/local/MATLAB/R2013a/toolbox/curvefit/splines
/usr/local/MATLAB/R2013a/toolbox/curvefit/cftoolgui
/usr/local/MATLAB/R2013a/toolbox/curvefit/sftoolgui
/usr/local/MATLAB/R2013a/toolbox/dsp/dspdemos
/usr/local/MATLAB/R2013a/toolbox/matlab/audiovideo
/usr/local/MATLAB/R2013a/help/toolbox/dsp/examples
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