Dear all,
I am currently trying to apply the preprocessing pipeline from Michael Notter’s tutorial (https://miykael.github.io/nipype_tutorial/notebooks/handson_preprocessing.html) to my data. I recreated the workflow but when running it breaks with “Error on “preproc_wf.susan.median”” and further it gives “Standard error:
Mask and image must be the same size”.
Below you find the output up to the error.
Thanks for your help in advance!
191114-11:44:35,831 nipype.workflow INFO: Workflow preproc_wf settings: ['check', 'execution', 'logging', 'monitoring'] 191114-11:44:35,848 nipype.workflow INFO: Running in parallel. 191114-11:44:35,853 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 28.06/28.06, Free processors: 4/4. 191114-11:44:35,960 nipype.workflow INFO: [Node] Setting-up "preproc_wf.datagrabber" in "/media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/datagrabber". 191114-11:44:35,997 nipype.workflow INFO: [Node] Running "datagrabber" ("nipype.interfaces.io.DataGrabber") 191114-11:44:36,13 nipype.workflow INFO: [Node] Finished "preproc_wf.datagrabber". 191114-11:44:37,858 nipype.workflow INFO: [Job 0] Completed (preproc_wf.datagrabber). 191114-11:44:37,868 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 28.06/28.06, Free processors: 4/4. 191114-11:44:37,985 nipype.workflow INFO: [Node] Setting-up "preproc_wf.gunzip_func" in "/media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/gunzip_func". 191114-11:44:37,990 nipype.workflow INFO: [Node] Running "gunzip_func" ("nipype.algorithms.misc.Gunzip") 191114-11:44:37,985 nipype.workflow INFO: [Node] Setting-up "preproc_wf.gunzip_anat" in "/media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/gunzip_anat". 191114-11:44:38,5 nipype.workflow INFO: [Node] Running "gunzip_anat" ("nipype.algorithms.misc.Gunzip") 191114-11:44:38,177 nipype.workflow INFO: [Node] Finished "preproc_wf.gunzip_anat". 191114-11:44:39,449 nipype.workflow INFO: [Node] Finished "preproc_wf.gunzip_func". 191114-11:44:39,858 nipype.workflow INFO: [Job 1] Completed (preproc_wf.gunzip_anat). 191114-11:44:39,863 nipype.workflow INFO: [Job 6] Completed (preproc_wf.gunzip_func). 191114-11:44:39,870 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 28.06/28.06, Free processors: 4/4. 191114-11:44:39,974 nipype.workflow INFO: [Node] Setting-up "preproc_wf.mcflirt" in "/media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/mcflirt". 191114-11:44:39,974 nipype.workflow INFO: [Node] Setting-up "preproc_wf.segment" in "/media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/segment". 191114-11:44:39,978 nipype.workflow INFO: [Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command: mcflirt -in /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/gunzip_func/DICOM_cmrr_mbep2d_bold_H20_44_MB2_20190930162755_10.nii -meanvol -out /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/mcflirt/DICOM_cmrr_mbep2d_bold_H20_44_MB2_20190930162755_10_mcf.nii.gz -plots 191114-11:44:39,981 nipype.workflow INFO: [Node] Running "segment" ("nipype.interfaces.spm.preprocess.NewSegment") 191114-11:44:41,858 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 27.66/28.06, Free processors: 2/4. Currently running: * preproc_wf.mcflirt * preproc_wf.segment 191114-11:47:33,114 nipype.workflow INFO: [Node] Finished "preproc_wf.mcflirt". 191114-11:47:34,16 nipype.workflow INFO: [Job 7] Completed (preproc_wf.mcflirt). 191114-11:47:34,18 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 27.86/28.06, Free processors: 3/4. Currently running: * preproc_wf.segment 191114-11:47:34,84 nipype.workflow INFO: [Node] Setting-up "preproc_wf.art" in "/media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/art". 191114-11:47:34,89 nipype.workflow INFO: [Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect") 191114-11:47:36,18 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 27.66/28.06, Free processors: 2/4. Currently running: * preproc_wf.art * preproc_wf.segment 191114-11:47:37,679 nipype.workflow INFO: [Node] Finished "preproc_wf.art". 191114-11:47:38,19 nipype.workflow INFO: [Job 18] Completed (preproc_wf.art). 191114-11:47:38,23 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 27.86/28.06, Free processors: 3/4. Currently running: * preproc_wf.segment 191114-11:47:50,347 nipype.workflow INFO: [Node] Finished "preproc_wf.segment". 191114-11:47:52,35 nipype.workflow INFO: [Job 2] Completed (preproc_wf.segment). 191114-11:47:52,42 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 28.06/28.06, Free processors: 4/4. 191114-11:47:52,104 nipype.workflow INFO: [Node] Setting-up "preproc_wf.resample" in "/media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/resample". 191114-11:47:52,104 nipype.workflow INFO: [Node] Setting-up "preproc_wf.threshold_WM" in "/media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/threshold_WM". 191114-11:47:52,109 nipype.workflow INFO: [Node] Running "resample" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command: flirt -in /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/segment/c1DICOM_t1_mprage_sag_fast_grappa2_20190930162755_11.nii -ref /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/segment/c1DICOM_t1_mprage_sag_fast_grappa2_20190930162755_11.nii -out c1DICOM_t1_mprage_sag_fast_grappa2_20190930162755_11_flirt.nii -omat c1DICOM_t1_mprage_sag_fast_grappa2_20190930162755_11_flirt.mat -applyisoxfm 4.000000 191114-11:47:52,110 nipype.workflow INFO: [Node] Running "threshold_WM" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command: fslmaths /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/segment/c2DICOM_t1_mprage_sag_fast_grappa2_20190930162755_11.nii -thr 0.5000000000 -bin /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/threshold_WM/c2DICOM_t1_mprage_sag_fast_grappa2_20190930162755_11_thresh.nii 191114-11:47:52,607 nipype.workflow INFO: [Node] Finished "preproc_wf.threshold_WM". 191114-11:47:54,35 nipype.workflow INFO: [Job 5] Completed (preproc_wf.threshold_WM). 191114-11:47:54,39 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 27.86/28.06, Free processors: 3/4. Currently running: * preproc_wf.resample 191114-11:47:54,104 nipype.workflow INFO: [Node] Setting-up "preproc_wf.coreg" in "/media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/coreg". 191114-11:47:54,111 nipype.workflow INFO: [Node] Running "coreg" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command: flirt -in /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/mcflirt/DICOM_cmrr_mbep2d_bold_H20_44_MB2_20190930162755_10_mcf_mean_reg.nii.gz -ref /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/gunzip_anat/DICOM_t1_mprage_sag_fast_grappa2_20190930162755_11.nii -out DICOM_cmrr_mbep2d_bold_H20_44_MB2_20190930162755_10_mcf_mean_reg_flirt.nii -omat DICOM_cmrr_mbep2d_bold_H20_44_MB2_20190930162755_10_mcf_mean_reg_flirt.mat -cost bbr -dof 6 -schedule /usr/local/fsl/etc/flirtsch/bbr.sch -wmseg /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/threshold_WM/c2DICOM_t1_mprage_sag_fast_grappa2_20190930162755_11_thresh.nii 191114-11:47:55,110 nipype.workflow INFO: [Node] Finished "preproc_wf.resample". 191114-11:47:56,37 nipype.workflow INFO: [Job 3] Completed (preproc_wf.resample). 191114-11:47:56,39 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 27.86/28.06, Free processors: 3/4. Currently running: * preproc_wf.coreg 191114-11:47:56,105 nipype.workflow INFO: [Node] Setting-up "preproc_wf.mask_GM" in "/media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/mask_GM". 191114-11:47:56,109 nipype.workflow INFO: [Node] Running "mask_GM" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command: fslmaths /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/resample/c1DICOM_t1_mprage_sag_fast_grappa2_20190930162755_11_flirt.nii -thr 0.5000000000 -bin -dilF /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/mask_GM/c1DICOM_t1_mprage_sag_fast_grappa2_20190930162755_11_flirt_thresh.nii 191114-11:47:56,364 nipype.workflow INFO: [Node] Finished "preproc_wf.mask_GM". 191114-11:47:58,39 nipype.workflow INFO: [Job 4] Completed (preproc_wf.mask_GM). 191114-11:47:58,41 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 27.86/28.06, Free processors: 3/4. Currently running: * preproc_wf.coreg 191114-11:48:45,397 nipype.workflow INFO: [Node] Finished "preproc_wf.coreg". 191114-11:48:46,90 nipype.workflow INFO: [Job 8] Completed (preproc_wf.coreg). 191114-11:48:46,97 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 28.06/28.06, Free processors: 4/4. 191114-11:48:46,169 nipype.workflow INFO: [Node] Setting-up "preproc_wf.applywarp" in "/media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/applywarp". 191114-11:48:46,175 nipype.workflow INFO: [Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command: flirt -in /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/mcflirt/DICOM_cmrr_mbep2d_bold_H20_44_MB2_20190930162755_10_mcf.nii.gz -ref /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/gunzip_anat/DICOM_t1_mprage_sag_fast_grappa2_20190930162755_11.nii -out DICOM_cmrr_mbep2d_bold_H20_44_MB2_20190930162755_10_mcf_flirt.nii -omat DICOM_cmrr_mbep2d_bold_H20_44_MB2_20190930162755_10_mcf_flirt.mat -applyisoxfm 4.000000 -init /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/coreg/DICOM_cmrr_mbep2d_bold_H20_44_MB2_20190930162755_10_mcf_mean_reg_flirt.mat -interp spline 191114-11:48:48,90 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 27.86/28.06, Free processors: 3/4. Currently running: * preproc_wf.applywarp 191114-11:50:36,333 nipype.workflow INFO: [Node] Finished "preproc_wf.applywarp". 191114-11:50:38,195 nipype.workflow INFO: [Job 9] Completed (preproc_wf.applywarp). 191114-11:50:38,202 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 28.06/28.06, Free processors: 4/4. 191114-11:50:38,268 nipype.workflow INFO: [Node] Setting-up "preproc_wf.susan.mask" in "/media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/susan/_run_id_1_subject_id_2/mask". 191114-11:50:38,270 nipype.workflow INFO: [Node] Setting-up "preproc_wf.susan.median" in "/media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/susan/_run_id_1_subject_id_2/median". 191114-11:50:38,272 nipype.workflow INFO: [Node] Setting-up "_mask0" in "/media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/susan/_run_id_1_subject_id_2/mask/mapflow/_mask0". 191114-11:50:38,275 nipype.workflow INFO: [Node] Running "_mask0" ("nipype.interfaces.fsl.utils.ImageMaths"), a CommandLine Interface with command: fslmaths /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/applywarp/DICOM_cmrr_mbep2d_bold_H20_44_MB2_20190930162755_10_mcf_flirt.nii -mas /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/mask_GM/c1DICOM_t1_mprage_sag_fast_grappa2_20190930162755_11_flirt_thresh.nii /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/susan/_run_id_1_subject_id_2/mask/mapflow/_mask0/DICOM_cmrr_mbep2d_bold_H20_44_MB2_20190930162755_10_mcf_flirt_mask.nii.gz 191114-11:50:38,276 nipype.workflow INFO: [Node] Setting-up "_median0" in "/media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/susan/_run_id_1_subject_id_2/median/mapflow/_median0". 191114-11:50:38,283 nipype.workflow INFO: [Node] Running "_median0" ("nipype.interfaces.fsl.utils.ImageStats"), a CommandLine Interface with command: fslstats /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/applywarp/DICOM_cmrr_mbep2d_bold_H20_44_MB2_20190930162755_10_mcf_flirt.nii -k /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/mask_GM/c1DICOM_t1_mprage_sag_fast_grappa2_20190930162755_11_flirt_thresh.nii -p 50 191114-11:50:39,339 nipype.workflow WARNING: Storing result file without outputs 191114-11:50:39,342 nipype.workflow WARNING: [Node] Error on "_median0" (/media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/susan/_run_id_1_subject_id_2/median/mapflow/_median0) 191114-11:50:39,345 nipype.workflow WARNING: [Node] Error on "preproc_wf.susan.median" (/media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/susan/_run_id_1_subject_id_2/median) exception calling callback for <Future at 0x7f6ea465f4e0 state=finished raised FileNotFoundError> concurrent.futures.process._RemoteTraceback: """ Traceback (most recent call last): File "/home/marius/anaconda3/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node result['result'] = node.run(updatehash=updatehash) File "/home/marius/anaconda3/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 479, in run result = self._run_interface(execute=True) File "/home/marius/anaconda3/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 1298, in _run_interface self.config['execution']['stop_on_first_crash']))) File "/home/marius/anaconda3/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 1220, in _collate_results (self.name, '\n'.join(msg))) Exception: Subnodes of node: median failed: Subnode 0 failed Error: Traceback (most recent call last): File "/home/marius/anaconda3/lib/python3.7/site-packages/nipype/pipeline/engine/utils.py", line 107, in nodelist_runner result = node.run(updatehash=updatehash) File "/home/marius/anaconda3/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 479, in run result = self._run_interface(execute=True) File "/home/marius/anaconda3/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 585, in _run_interface return self._run_command(execute) File "/home/marius/anaconda3/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 678, in _run_command result = self._interface.run(cwd=outdir) File "/home/marius/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 382, in run runtime = self._run_interface(runtime) File "/home/marius/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 767, in _run_interface self.raise_exception(runtime) File "/home/marius/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 704, in raise_exception ).format(**runtime.dictcopy())) RuntimeError: Command: fslstats /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/applywarp/DICOM_cmrr_mbep2d_bold_H20_44_MB2_20190930162755_10_mcf_flirt.nii -k /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/_run_id_1_subject_id_2/mask_GM/c1DICOM_t1_mprage_sag_fast_grappa2_20190930162755_11_flirt_thresh.nii -p 50 Standard output: Standard error: Mask and image must be the same size Return code: 3 During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/marius/anaconda3/lib/python3.7/concurrent/futures/process.py", line 232, in _process_worker r = call_item.fn(*call_item.args, **call_item.kwargs) File "/home/marius/anaconda3/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 72, in run_node result['result'] = node.result File "/home/marius/anaconda3/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 198, in result op.join(self.output_dir(), 'result_%s.pklz' % self.name)) File "/home/marius/anaconda3/lib/python3.7/site-packages/nipype/pipeline/engine/utils.py", line 304, in load_resultfile raise FileNotFoundError(results_file) FileNotFoundError: /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/susan/_run_id_1_subject_id_2/median/result_median.pklz """ The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/marius/anaconda3/lib/python3.7/concurrent/futures/_base.py", line 324, in _invoke_callbacks callback(self) File "/home/marius/anaconda3/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 149, in _async_callback result = args.result() File "/home/marius/anaconda3/lib/python3.7/concurrent/futures/_base.py", line 425, in result return self.__get_result() File "/home/marius/anaconda3/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result raise self._exception FileNotFoundError: /media/marius/data/experimental_data/arrow_gaze/participants_data/datasink/preproc_wf/susan/_run_id_1_subject_id_2/median/result_median.pklz