Merge = pe.Node(interface=fsl.Merge(), name="merge") Use :class:`` to merge a series of 3D files along the time Variable, because switching between 3d and 4d requires some additional steps (explauned later on). Therefore we leave converting to 4D as an option. The the workflow presented in the SPM8 manual which this tutorial is based on """We strongly encourage to use 4D files insteead of series of 3D for fMRI analysesįor many reasons (cleanness and saving and filesystem inodes are among them). This is a generic preprocessing workflow that can be used by different analyses This will demonstrate how pre-defined workflows can be setupĪnd shared across users, projects and labs. In this tutorial we will be setting up a hierarchical workflow for spmĪnalysis. #_default_paths('/home/ankita/spmsoft/spm12/spm.m') _default_matlab_cmd("matlab -nodesktop -nosplash") The fmri_spm_auditory.py recreates the classical workflow described in the # emacs: -*- mode: python py-indent-offset: 4 indent-tabs-mode: nil -*. No executable modules, but still unresolved dependencies or incomplete module inputs.įile:/usr/local/MATLAB/R2016b/toolbox/spm12/spm_jobman.m SPM path: /usr/local/MATLAB/R2016b/toolbox/spm12/spm.mĬonversion Normalise:Write -> Old Normalise:Write System Identification Toolbox Version 9.5 (R2016b) Symbolic Math Toolbox Version 7.1 (R2016b) Statistics and Machine Learning Toolbox Version 11.0 (R2016b) Statistical Parametric Mapping Version 6906 (SPM12) Simulink Control Design Version 4.4 (R2016b) Simulink 3D Animation Version 7.6 (R2016b) Simscape Electronics Version 2.10 (R2016b) Signal Processing Toolbox Version 7.3 (R2016b) Robust Control Toolbox Version 6.2 (R2016b) Robotics System Toolbox Version 1.3 (R2016b) Phased Array System Toolbox Version 3.3 (R2016b) Partial Differential Equation Toolbox Version 2.3 (R2016b) Parallel Computing Toolbox Version 6.9 (R2016b) Optimization Toolbox Version 7.5 (R2016b) Neural Network Toolbox Version 9.1 (R2016b) Model Predictive Control Toolbox Version 5.2.1 (R2016b) MATLAB Report Generator Version 5.1 (R2016b) Instrument Control Toolbox Version 3.10 (R2016b) Image Processing Toolbox Version 9.5 (R2016b) Image Acquisition Toolbox Version 5.1 (R2016b) Global Optimization Toolbox Version 3.4.1 (R2016b) Java Version: Java 1.7.0_60-b19 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed modeĪudio System Toolbox Version 1.1 (R2016b)īioinformatics Toolbox Version 4.7 (R2016b)Ĭommunications System Toolbox Version 6.3 (R2016b)Ĭomputer Vision System Toolbox Version 7.2 (R2016b)Ĭontrol System Toolbox Version 10.1 (R2016b)Ĭurve Fitting Toolbox Version 3.5.4 (R2016b)įilter Design HDL Coder Version 3.1 (R2016b)įixed-Point Designer Version 5.3 (R2016b)įuzzy Logic Toolbox Version 2.2.24 (R2016b) To get started, type one of these: helpwin, helpdesk, or demo.įor product information, visit Executing pyscript_normalize at 2 02:38:17: MATLAB is selecting SOFTWARE OPENGL rendering. Matlab -nodesktop -nosplash -nodesktop -nosplash -singleCompThread -r "addpath('/home/ankita/preprocess/spm_auditory_tutorial/workingdir/level1/firstlevel/preproc/_subject_id_M00223/normalize_struc') pyscript_normalize exit" Self._result = self._run_command(execute)įile "/home/ankita/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 607, in _run_commandįile "/home/ankita/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1085, in runįile "/home/ankita/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1033, in _run_wrapperįile "/home/ankita/anaconda2/lib/python2.7/site-packages/nipype/interfaces/spm/base.py", line 323, in _run_interfaceįile "/home/ankita/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1728, in _run_wrapperįile "/home/ankita/anaconda2/lib/python2.7/site-packages/nipype/interfaces/matlab.py", line 152, in _run_interfaceįile "/home/ankita/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1686, in raise_exception Parameter_file = /home/ankita/preprocess/spm_auditory_tutorial/workingdir/level1/firstlevel/preproc/_subject_id_M00223/normalize_struc/sM00223_002_seg_sn.matįile "/home/ankita/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 43, in runįile "/home/ankita/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 366, in runįile "/home/ankita/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 476, in _run_interface Working directory: /home/ankita/preprocess/spm_auditory_tutorial/workingdir/level1/firstlevel/preproc/_subject_id_M00223/normalize_struc
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |