i am new to nipy. i was learning pipeline using frmi_spm_auditory code from ur github page. i am getting this error in my crash file when i am running it. please help.
From my understanding its giving error since cant found spm on its path but I checked its there.
I run these commands:
import nipype.interfaces.spm as spm
spm.Info.version()
its giving this output-
{u’name’: u’SPM12’,
u’path’: u’/home/ankita/spmsoft/spm12’,
u’release’: u’6906’}
Crash file produced:
File: crash-20170310-011734-ankita-realign.a0-db81fe36-9277-4276-99e1-f6b77617e2b3.pklz
Node: level1.firstlevel.preproc.realign.a0
Working directory: /home/ankita/Downloads/preprocess/spm_auditory_tutorial/workingdir/level1/firstlevel/preproc/_subject_id_M00223/realign
Node inputs:
fwhm =
ignore_exception = False
in_files = [’/home/ankita/Downloads/preprocess/spm_auditory_tutorial/workingdir/level1/firstlevel/preproc/_subject_id_M00223/realign/fM00223_016.img’, ‘/home/ankita/Downloads/preprocess/spm_auditory_tutorial/workingdir/level1/firstlevel/preproc/_subject_id_M00223/realign/fM00223_017.img’, ‘/home/ankita/Downloads/preprocess/spm_auditory_tutorial/workingdir/level1/firstlevel/preproc/_subject_id_M00223/realign/fM00223_018.img’, ‘/home/ankita/Downloads/preprocess/spm_auditory_tutorial/workingdir/level1/firstlevel/preproc/_subject_id_M00223/realign/fM00223_019.img’, ‘/home/ankita/Downloads/preprocess/spm_auditory_tutorial/workingdir/level1/firstlevel/preproc/_subject_id_M00223/realign/fM00223_020.img’, ‘/home/ankita/Downloads/preprocess/spm_auditory_tutorial/workingdir/level1/firstlevel/preproc/_subject_id_M00223/realign/fM00223_021.img’, ‘/home/ankita/Downloads/preprocess/spm_auditory_tutorial/workingdir/level1/firstlevel/preproc/_subject_id_M00223/realign/fM00223_022.img’, 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interp =
jobtype = estwrite
matlab_cmd =
mfile = True
out_prefix = r
paths =
quality =
register_to_mean =
separation =
use_mcr =
use_v8struct = True
weight_img =
wrap =
write_interp =
write_mask =
write_which = [2, 1]
write_wrap =
Traceback:
Traceback (most recent call last):
File “/home/ankita/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py”, line 39, in run
node.run(updatehash=updatehash)
File “/home/ankita/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py”, line 394, in run
self._run_interface()
File “/home/ankita/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py”, line 504, in _run_interface
self._result = self._run_command(execute)
File “/home/ankita/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py”, line 630, in _run_command
result = self._interface.run()
File “/home/ankita/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py”, line 1043, in run
runtime = self._run_wrapper(runtime)
File “/home/ankita/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py”, line 1000, in _run_wrapper
runtime = self._run_interface(runtime)
File “/home/ankita/anaconda2/lib/python2.7/site-packages/nipype/interfaces/spm/base.py”, line 311, in _run_interface
results = self.mlab.run()
File “/home/ankita/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py”, line 1043, in run
runtime = self._run_wrapper(runtime)
File “/home/ankita/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py”, line 1660, in _run_wrapper
runtime = self._run_interface(runtime)
File “/home/ankita/anaconda2/lib/python2.7/site-packages/nipype/interfaces/matlab.py”, line 149, in _run_interface
self.raise_exception(runtime)
File “/home/ankita/anaconda2/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(’/home/ankita/Downloads/preprocess/spm_auditory_tutorial/workingdir/level1/firstlevel/preproc/_subject_id_M00223/realign’);pyscript_realign;exit”
Standard output:
MATLAB is selecting SOFTWARE OPENGL rendering.
< M A T L A B (R) >
Copyright 1984-2016 The MathWorks, Inc.
R2016b (9.1.0.441655) 64-bit (glnxa64)
September 7, 2016
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Executing pyscript_realign at 10-Mar-2017 01:17:31:
MATLAB Version: 9.1.0.441655 (R2016b)
MATLAB License Number: 40480989
Operating System: Linux 3.16.0-60-generic #80~14.04.1-Ubuntu SMP Wed Jan 20 13:37:48 UTC 2016 x86_64
Java Version: Java 1.7.0_60-b19 with Oracle Corporation Java HotSpot™ 64-Bit Server VM mixed mode
MATLAB Version 9.1 (R2016b)
Simulink Version 8.8 (R2016b)
Antenna Toolbox Version 2.1 (R2016b)
Audio System Toolbox Version 1.1 (R2016b)
Bioinformatics Toolbox Version 4.7 (R2016b)
Communications System Toolbox Version 6.3 (R2016b)
Computer Vision System Toolbox Version 7.2 (R2016b)
Control System Toolbox Version 10.1 (R2016b)
Curve Fitting Toolbox Version 3.5.4 (R2016b)
DSP System Toolbox Version 9.3 (R2016b)
Database Toolbox Version 7.0 (R2016b)
Embedded Coder Version 6.11 (R2016b)
Filter Design HDL Coder Version 3.1 (R2016b)
Fixed-Point Designer Version 5.3 (R2016b)
Fuzzy Logic Toolbox Version 2.2.24 (R2016b)
Global Optimization Toolbox Version 3.4.1 (R2016b)
HDL Coder Version 3.9 (R2016b)
HDL Verifier Version 5.1 (R2016b)
Image Acquisition Toolbox Version 5.1 (R2016b)
Image Processing Toolbox Version 9.5 (R2016b)
Instrument Control Toolbox Version 3.10 (R2016b)
LTE System Toolbox Version 2.3 (R2016b)
MATLAB Coder Version 3.2 (R2016b)
MATLAB Report Generator Version 5.1 (R2016b)
Mapping Toolbox Version 4.4 (R2016b)
Model Predictive Control Toolbox Version 5.2.1 (R2016b)
Neural Network Toolbox Version 9.1 (R2016b)
Optimization Toolbox Version 7.5 (R2016b)
Parallel Computing Toolbox Version 6.9 (R2016b)
Partial Differential Equation Toolbox Version 2.3 (R2016b)
Phased Array System Toolbox Version 3.3 (R2016b)
RF Toolbox Version 3.1 (R2016b)
Robotics System Toolbox Version 1.3 (R2016b)
Robust Control Toolbox Version 6.2 (R2016b)
Signal Processing Toolbox Version 7.3 (R2016b)
SimRF Version 5.1 (R2016b)
Simscape Version 4.1 (R2016b)
Simscape Driveline Version 2.11 (R2016b)
Simscape Electronics Version 2.10 (R2016b)
Simscape Multibody Version 4.9 (R2016b)
Simulink 3D Animation Version 7.6 (R2016b)
Simulink Control Design Version 4.4 (R2016b)
Stateflow Version 8.8 (R2016b)
Statistics and Machine Learning Toolbox Version 11.0 (R2016b)
Symbolic Math Toolbox Version 7.1 (R2016b)
System Identification Toolbox Version 9.5 (R2016b)
WLAN System Toolbox Version 1.2 (R2016b)
Wavelet Toolbox Version 4.17 (R2016b)
Standard error:
MATLAB code threw an exception:
SPM not in matlab path
File:/home/ankita/Downloads/preprocess/spm_auditory_tutorial/workingdir/level1/firstlevel/preproc/_subject_id_M00223/realign/pyscript_realign.m
Name:pyscript_realign
Line:6
Return code: 0
Interface MatlabCommand failed to run.
Interface Realign failed to run.