Hi all,
I am trying to realign 4D nifti image with SPM Standalone (version 12). The code is working fine with SPM12 with licensed MATLAB in mac. But I am getting error when I use SPM Standalone in ubuntu 18.04 os (it’s in VM). Sometimes the editor (Pycharm) exits without showing any error. Can anyone please tell me what I am doing wrong here? Thanks in advance.
Here is the code:
from nipype.interfaces import spm
matlab_cmd = ‘/home/ruba/Documents/spm_installation/spm12/run_spm12.sh /usr/local/MATLAB/MATLAB_Runtime/v97/ script’
spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
print(spm.SPMCommand.version)
list_of_file = [’/home/ruba/PycharmProjects/testPipeline/Input_data/h4003mame1/pet/result/source_frame_4_nac.nii’,
‘/home/ruba/PycharmProjects/testPipeline/Input_data/h4003mame1/pet/result/source_frame_5_nac.nii’,
‘/home/ruba/PycharmProjects/testPipeline/Input_data/h4003mame1/pet/result/source_frame_6_nac.nii’,
‘/home/ruba/PycharmProjects/testPipeline/Input_data/h4003mame1/pet/result/source_frame_7_nac.nii’,
‘/home/ruba/PycharmProjects/testPipeline/Input_data/h4003mame1/pet/result/source_frame_8_nac.nii’,
‘/home/ruba/PycharmProjects/testPipeline/Input_data/h4003mame1/pet/result/source_frame_9_nac.nii’,
‘/home/ruba/PycharmProjects/testPipeline/Input_data/h4003mame1/pet/result/source_frame_10_nac.nii’,
‘/home/ruba/PycharmProjects/testPipeline/Input_data/h4003mame1/pet/result/source_frame_11_nac.nii’,
‘/home/ruba/PycharmProjects/testPipeline/Input_data/h4003mame1/pet/result/source_frame_12_nac.nii’,
‘/home/ruba/PycharmProjects/testPipeline/Input_data/h4003mame1/pet/result/source_frame_13_nac.nii’]
realign = spm.Realign()
realign.inputs.in_files = list_of_file
realign.inputs.jobtype = ‘estimate’
realign.inputs.fwhm = 3.0
realign.inputs.quality = 1
realign.inputs.separation = 2
realign.inputs.interp = 1
realign.inputs.wrap = [0, 0, 0]
realign.inputs.register_to_mean = True
realign.run()
print(‘done’)
The error:
RuntimeError: Command:
/home/ruba/Documents/spm_installation/spm12/run_spm12.sh /usr/local/MATLAB/MATLAB_Runtime/v97/ script /home/ruba/PycharmProjects/testPipeline/Input_data/h3814smmi1/pet/pyscript_realign.m
Standard output:
Setting up environment variables
LD_LIBRARY_PATH is .:/usr/local/MATLAB/MATLAB_Runtime/v97//runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v97//bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v97//sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v97//sys/opengl/lib/glnxa64
SPM12, version 7771 (standalone)
MATLAB, version 9.7.0.1434023 (R2019b) Update 6
/ )( _ ( / )
_ \ )/ ) ( Statistical Parametric Mapping
(/(_) (_//_) SPM12 - https://www.fil.ion.ucl.ac.uk/spm/
Executing /home/ruba/PycharmProjects/testPipeline/Input_data/h3814smmi1/pet/pyscript_realign.m at 12-Aug-2020 16:16:22:
MATLAB Version: 9.7.0.1434023 (R2019b) Update 6
MATLAB License Number: unknown
Operating System: Linux 5.3.0-28-generic #30~18.04.1-Ubuntu SMP Fri Jan 17 06:14:09 UTC 2020 x86_64
Java Version: Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot™ 64-Bit Server VM mixed mode
MATLAB Version 9.7 (R2019b)
MATLAB Compiler Version 7.1 (R2019b)
SPM version: SPM12 Release: 7771
SPM path: /home/ruba/Documents/spm_installation/spm12/spm12_mcr/spm12/spm12/spm.m
Item estimate: No field(s) named
roptions
12-Aug-2020 16:16:31 - Running job #1
12-Aug-2020 16:16:31 - Running ‘Realign: Estimate’
SPM12: spm_realign (v7141) 16:16:31 - 12/08/2020
========================================================================
Standard error:
Killed
Return code: 137