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CoBrALab / RABIES

fMRI preprocessing pipeline and analysis tools adapted for rodent images. Visit the full documentation at https://rabies.readthedocs.io/en/stable/
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Running rabies analysis on docker #91

Closed ChristianNSchmitz closed 3 years ago

ChristianNSchmitz commented 4 years ago

Dear rabies-team, I would like to ask you if the docker-version of rabies is able to run other processing steps than preprocessing. I would like to run "rabies analysis" but cannot run it on docker. Best wishes Christian

Gab-D-G commented 4 years ago

Hi Christian, the latest version hasn't been updated to docker hub unfortunately but it will be available shortly! I will let you when it is ready.

Gab-D-G commented 4 years ago

The most recent version with both the confound regression and analysis workflows is now available in the docker version 0.2.0. You can try it out and let me know if it works out! Best, Gabe

ChristianNSchmitz commented 4 years ago

Dear Gabe, thanks a lot for updating it so quickly! Running the "confound_regression" part of the analysis I get the following error:

christian:~# docker run -it --rm -v /mnt/d/PsiAlc/Test/outputPreprocess/:/niiinputs:ro -v /mnt/d/PsiAlc/Test/outputConfoundRegression:/outputs gabdesgreg/rabies:latest confound_regression /niiinputs /outputs
Traceback (most recent call last):
  File "/home/rabies/RABIES-0.2.0/exec.py", line 13, in <module>
    execute_workflow()
  File "/home/rabies/RABIES-0.2.0/rabies/run_main.py", line 305, in execute_workflow
    workflow = confound_regression(opts, None, log)
  File "/home/rabies/RABIES-0.2.0/rabies/run_main.py", line 414, in confound_regression
    workflow = preprocess(preprocess_opts, opts, analysis_opts, log)
  File "/home/rabies/RABIES-0.2.0/rabies/run_main.py", line 385, in preprocess
    opts, cr_opts=cr_opts, analysis_opts=analysis_opts)
  File "/home/rabies/RABIES-0.2.0/rabies/main_wf.py", line 128, in init_main_wf
    layout, opts.bold_only)
  File "/home/rabies/RABIES-0.2.0/rabies/preprocess_pkg/utils.py", line 32, in prep_bids_iter
    "No anatomical file with the suffix 'T2w' or 'T1w' were found among the BIDS directory.")
ValueError: No anatomical file with the suffix 'T2w' or 'T1w' were found among the BIDS directory.

I am using the preprocessing directory as input for the confound_regression. This does not include the original 'T2w" or 'T1w' anatomical files.

Gab-D-G commented 4 years ago

Hi Christian, With the latest updates, there are some required BIDS specifications for the inputs. From the updated README: "Input folder must follow the BIDS structure (https://bids.neuroimaging.io/). RABIES will iterate through subjects and search for all available functional scans with suffix 'bold' or 'cbv'. If anatomical scans are used for preprocessing (--bold_only False), each functional scan will be matched to one corresponding anatomical scan with suffix 'T1w' or 'T2w' of the same subject/session."

Best, Gabe

kevinWinterburn commented 3 years ago

Hi, I am also getting the exact same error. How do I turn the output from preprocessing to BIDS structure? All the best, Kevin.

ChristianNSchmitz commented 3 years ago

Dear Gabe, I still have trouble with the right input format running the "confound_regression" part. Moreover, I noticed that the preprocessing of the dataset only works if all metadata is omitted. However, if I have a BIDS-compliant dataset containing the appropriate metadata, the preprocessing doesn't work properly. Best, Christian

Gab-D-G commented 3 years ago

Hi Christian, Kevin,

My appologies Christian if I didn't notice on the previous post that you were attempting to run the confound regression step. Did you try to run confound regression on a preprocessing output from a previous version of RABIES? When you update to a more recent version, I would generally advice to re-run the processing from the beginning to avoid such errors. Let me know if this is not your issue.

To make sure the syntax is appropriate, I would recommend following this example dataset as a template https://zenodo.org/record/3937697#.X42M9HVKg5k. That dataset shouldn't give errors.

Concerning the metadata issue, do you have more details on what gives rise to errors more exactly? I believe that BIDS compliant datasets with or without the metadata should work.

Best, Gabe

kevinWinterburn commented 3 years ago

Hi Gabe,

Unfortunately, I don't think is my issue - I ran the preprocesses on the same version as the confound regression. I am actually trying to run the confound regression on the test dataset that you linked! I am learning how to use RABIES for my FYP, so I am still quite unfamiliar with it.

Thanks for the help, Kevin.

On 19 Oct 2020, at 2:04 p.m., Gabriel Desrosiers-Gregoire notifications@github.com wrote:

Hi Christian, Kevin,

My appologies Christian if I didn't notice on the previous post that you were attempting to run the confound regression step. Did you try to run confound regression on a preprocessing output from a previous version of RABIES? When you update to a more recent version, I would generally advice to re-run the processing from the beginning to avoid such errors. Let me know if this is not your issue.

To make sure the syntax is appropriate, I would recommend following this example dataset as a template https://zenodo.org/record/3937697#.X42M9HVKg5k https://zenodo.org/record/3937697#.X42M9HVKg5k. That dataset shouldn't give errors.

Concerning the metadata issue, do you have more details on what gives rise to errors more exactly? I believe that BIDS compliant datasets with or without the metadata should work.

Best, Gabe

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/CoBrALab/RABIES/issues/91#issuecomment-712141885, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF7F6C36TLF5IBYZ6M4TINTSLQ2N5ANCNFSM4R7BUD3Q.

ChristianNSchmitz commented 3 years ago

Dear Gabe, I ran the confound regression step on preprocessing data of the older docker version. Updating the data resolved the issue, thanks a lot for that remark! However, BIDS compliant datasets with metadata gave me quite some trouble, even though the BIDS-validator worked. Best, Christian

ChristianNSchmitz commented 3 years ago

Dear Gabe, I have issues using another atlas for rats (SIGMA atlas) on the new docker version, can you make any sense out of this error message? The older docker version worked flawlessly with this atlas and looking at the images, both atlas and structural data appear to be coregistered perfectly. Moreover, the error message directs me to a crash log, however I cannot find that log file.

root@CaAH2a:~# docker run -it --rm -v /mnt/d/PsiAlc/Test/testAtlas/:/atlas -v /mnt/d/PsiAlc/RabiesDir/rawdata3/:/niiinputs:ro -v /mnt/d/PsiAlc/RabiesDir/derivates/outputPreprocess:/outputs gabdesgreg/rabies:latest preprocess /niiinputs /outputs --anat_template /atlas/SIGMA_InVivo_Brain_Template.nii --brain_mask /atlas/SIGMA_InVivo_Brain_Mask.nii --WM_mask /atlas/SIGMA_InVivo_WM.nii --CSF_mask /atlas/SIGMA_InVivo_CSF.nii --labels /atlas/SIGMA_Anatomical_Brain_Atlas.nii Running workflow with Linear plugin. 201101-06:43:57,621 nipype.workflow INFO: Workflow main_wf settings: ['check', 'execution', 'logging', 'monitoring'] 201101-06:43:58,176 nipype.workflow INFO: Running serially. 201101-06:43:58,178 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_selectfiles" in "/outputs/main_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/bold_selectfiles". 201101-06:43:58,288 nipype.workflow INFO: [Node] Cached "main_wf.bold_selectfiles" - collecting precomputed outputs 201101-06:43:58,289 nipype.workflow INFO: [Node] "main_wf.bold_selectfiles" found cached. 201101-06:43:58,289 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_convert_to_RAS" in "/outputs/main_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/bold_convert_to_RAS". 201101-06:43:58,331 nipype.workflow INFO: [Node] Cached "main_wf.bold_convert_to_RAS" - collecting precomputed outputs 201101-06:43:58,332 nipype.workflow INFO: [Node] "main_wf.bold_convert_to_RAS" found cached. 201101-06:43:58,332 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_stc_wf.slice_timing_correction" in "/outputs/main_wf/bold_main_wf/bold_stc_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/slice_timing_correction". 201101-06:43:58,383 nipype.workflow INFO: [Node] Cached "main_wf.bold_main_wf.bold_stc_wf.slice_timing_correction" - collecting precomputed outputs 201101-06:43:58,383 nipype.workflow INFO: [Node] "main_wf.bold_main_wf.bold_stc_wf.slice_timing_correction" found cached. 201101-06:43:58,384 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.gen_bold_ref.gen_ref" in "/outputs/main_wf/bold_main_wf/gen_bold_ref/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/gen_ref". 201101-06:43:58,432 nipype.workflow INFO: [Node] Cached "main_wf.bold_main_wf.gen_bold_ref.gen_ref" - collecting precomputed outputs 201101-06:43:58,433 nipype.workflow INFO: [Node] "main_wf.bold_main_wf.gen_bold_ref.gen_ref" found cached. 201101-06:43:58,433 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_hmc_wf.ants_MC" in "/outputs/main_wf/bold_main_wf/bold_hmc_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/ants_MC". 201101-06:43:58,511 nipype.workflow INFO: [Node] Cached "main_wf.bold_main_wf.bold_hmc_wf.ants_MC" - collecting precomputed outputs 201101-06:43:58,511 nipype.workflow INFO: [Node] "main_wf.bold_main_wf.bold_hmc_wf.ants_MC" found cached. 201101-06:43:58,512 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_selectfiles" in "/outputs/main_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/bold_selectfiles". 201101-06:43:58,545 nipype.workflow INFO: [Node] Cached "main_wf.bold_selectfiles" - collecting precomputed outputs 201101-06:43:58,546 nipype.workflow INFO: [Node] "main_wf.bold_selectfiles" found cached. 201101-06:43:58,547 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_convert_to_RAS" in "/outputs/main_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/bold_convert_to_RAS". 201101-06:43:58,582 nipype.workflow INFO: [Node] Cached "main_wf.bold_convert_to_RAS" - collecting precomputed outputs 201101-06:43:58,582 nipype.workflow INFO: [Node] "main_wf.bold_convert_to_RAS" found cached. 201101-06:43:58,583 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_stc_wf.slice_timing_correction" in "/outputs/main_wf/bold_main_wf/bold_stc_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/slice_timing_correction". 201101-06:43:58,628 nipype.workflow INFO: [Node] Cached "main_wf.bold_main_wf.bold_stc_wf.slice_timing_correction" - collecting precomputed outputs 201101-06:43:58,629 nipype.workflow INFO: [Node] "main_wf.bold_main_wf.bold_stc_wf.slice_timing_correction" found cached. 201101-06:43:58,629 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.gen_bold_ref.gen_ref" in "/outputs/main_wf/bold_main_wf/gen_bold_ref/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/gen_ref". 201101-06:43:58,678 nipype.workflow INFO: [Node] Cached "main_wf.bold_main_wf.gen_bold_ref.gen_ref" - collecting precomputed outputs 201101-06:43:58,679 nipype.workflow INFO: [Node] "main_wf.bold_main_wf.gen_bold_ref.gen_ref" found cached. 201101-06:43:58,679 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_hmc_wf.ants_MC" in "/outputs/main_wf/bold_main_wf/bold_hmc_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/ants_MC". 201101-06:43:58,763 nipype.workflow INFO: [Node] Cached "main_wf.bold_main_wf.bold_hmc_wf.ants_MC" - collecting precomputed outputs 201101-06:43:58,763 nipype.workflow INFO: [Node] "main_wf.bold_main_wf.bold_hmc_wf.ants_MC" found cached. 201101-06:43:58,764 nipype.workflow INFO: [Node] Setting-up "main_wf.anat_selectfiles" in "/outputs/main_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/anat_selectfiles". 201101-06:43:58,792 nipype.workflow INFO: [Node] Cached "main_wf.anat_selectfiles" - collecting precomputed outputs 201101-06:43:58,792 nipype.workflow INFO: [Node] "main_wf.anat_selectfiles" found cached. 201101-06:43:58,793 nipype.workflow INFO: [Node] Setting-up "main_wf.anat_convert_to_RAS" in "/outputs/main_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/anat_convert_to_RAS". 201101-06:43:58,831 nipype.workflow INFO: [Node] Cached "main_wf.anat_convert_to_RAS" - collecting precomputed outputs 201101-06:43:58,832 nipype.workflow INFO: [Node] "main_wf.anat_convert_to_RAS" found cached. 201101-06:43:58,832 nipype.workflow INFO: [Node] Setting-up "main_wf.anat_selectfiles" in "/outputs/main_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/anat_selectfiles". 201101-06:43:58,865 nipype.workflow INFO: [Node] Cached "main_wf.anat_selectfiles" - collecting precomputed outputs 201101-06:43:58,865 nipype.workflow INFO: [Node] "main_wf.anat_selectfiles" found cached. 201101-06:43:58,866 nipype.workflow INFO: [Node] Setting-up "main_wf.anat_convert_to_RAS" in "/outputs/main_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/anat_convert_to_RAS". 201101-06:43:58,906 nipype.workflow INFO: [Node] Cached "main_wf.anat_convert_to_RAS" - collecting precomputed outputs 201101-06:43:58,906 nipype.workflow INFO: [Node] "main_wf.anat_convert_to_RAS" found cached. 201101-06:43:58,907 nipype.workflow INFO: [Node] Setting-up "main_wf.resample_template" in "/outputs/main_wf/resample_template". 201101-06:43:58,930 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.resample_template". 201101-06:43:58,965 nipype.workflow INFO: [Node] Running "resample_template" ("nipype.interfaces.utility.wrappers.Function") Resampling template to 0.15003332495689392x0.15003332495689392x0.15003332495689392mm dimensions. 201101-06:44:00,352 nipype.workflow INFO: [Node] Finished "main_wf.resample_template". 201101-06:44:00,352 nipype.workflow INFO: [Node] Setting-up "main_wf.anat_preproc_wf.Anat_Preproc" in "/outputs/main_wf/anat_preproc_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/Anat_Preproc". 201101-06:44:00,384 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.anat_preproc_wf.Anat_Preproc". 201101-06:44:00,448 nipype.workflow INFO: [Node] Running "Anat_Preproc" ("rabies.preprocess_pkg.anat_preproc.AnatPreproc") Anat image will be resampled to the template resolution. 201101-06:50:33,846 nipype.workflow INFO: [Node] Finished "main_wf.anat_preproc_wf.Anat_Preproc". 201101-06:50:33,847 nipype.workflow INFO: [Node] Setting-up "main_wf.anat_preproc_wf.Anat_Preproc" in "/outputs/main_wf/anat_preproc_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/Anat_Preproc". 201101-06:50:33,876 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.anat_preproc_wf.Anat_Preproc". 201101-06:50:33,920 nipype.workflow INFO: [Node] Running "Anat_Preproc" ("rabies.preprocess_pkg.anat_preproc.AnatPreproc") Anat image will be resampled to the template resolution. 201101-06:56:45,913 nipype.workflow INFO: [Node] Finished "main_wf.anat_preproc_wf.Anat_Preproc". 201101-06:56:45,913 nipype.workflow INFO: [Node] Setting-up "main_wf.commonspace_reg" in "/outputs/main_wf/commonspace_reg". 201101-06:56:46,13 nipype.workflow INFO: [Node] Running "commonspace_reg" ("rabies.preprocess_pkg.commonspace.ANTsDBM") Previous ants_dbm_outputs/ folder detected. Inputs from a previous run may cause issues for the commonspace registration, so consider removing the previous folder before running again. 201101-06:56:56,35 nipype.workflow INFO: [Node] Finished "main_wf.commonspace_reg". 201101-06:56:56,37 nipype.workflow INFO: [Node] Setting-up "main_wf.commonspace_selectfiles" in "/outputs/main_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/commonspace_selectfiles". 201101-06:56:56,168 nipype.workflow INFO: [Node] Cached "main_wf.commonspace_selectfiles" - collecting precomputed outputs 201101-06:56:56,169 nipype.workflow INFO: [Node] "main_wf.commonspace_selectfiles" found cached. 201101-06:56:56,169 nipype.workflow INFO: [Node] Setting-up "main_wf.PlotOverlap_Anat2Template" in "/outputs/main_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/PlotOverlap_Anat2Template". 201101-06:56:56,239 nipype.workflow INFO: [Node] Cached "main_wf.PlotOverlap_Anat2Template" - collecting precomputed outputs 201101-06:56:56,239 nipype.workflow INFO: [Node] "main_wf.PlotOverlap_Anat2Template" found cached. 201101-06:56:56,240 nipype.workflow INFO: [Node] Setting-up "main_wf.commonspace_selectfiles" in "/outputs/main_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/commonspace_selectfiles". 201101-06:56:56,359 nipype.workflow INFO: [Node] Cached "main_wf.commonspace_selectfiles" - collecting precomputed outputs 201101-06:56:56,359 nipype.workflow INFO: [Node] "main_wf.commonspace_selectfiles" found cached. 201101-06:56:56,360 nipype.workflow INFO: [Node] Setting-up "main_wf.PlotOverlap_Anat2Template" in "/outputs/main_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/PlotOverlap_Anat2Template". 201101-06:56:56,431 nipype.workflow INFO: [Node] Cached "main_wf.PlotOverlap_Anat2Template" - collecting precomputed outputs 201101-06:56:56,432 nipype.workflow INFO: [Node] "main_wf.PlotOverlap_Anat2Template" found cached. 201101-06:56:56,432 nipype.workflow INFO: [Node] Setting-up "main_wf.template_reg" in "/outputs/main_wf/template_reg". 201101-06:56:56,461 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.template_reg". 201101-06:56:56,493 nipype.workflow INFO: [Node] Running "template_reg" ("nipype.interfaces.utility.wrappers.Function") 201101-07:19:22,704 nipype.workflow INFO: [Node] Finished "main_wf.template_reg". 201101-07:19:22,704 nipype.workflow INFO: [Node] Setting-up "main_wf.transform_masks" in "/outputs/main_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/transform_masks". 201101-07:19:22,774 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.transform_masks". 201101-07:19:22,851 nipype.workflow INFO: [Node] Running "transform_masks" ("nipype.interfaces.utility.wrappers.Function") 201101-07:26:50,544 nipype.workflow INFO: [Node] Finished "main_wf.transform_masks". 201101-07:26:50,544 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bias_correction_wf.bias_correction" in "/outputs/main_wf/bold_main_wf/bias_correction_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/bias_correction". 201101-07:26:50,619 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bias_correction_wf.bias_correction". 201101-07:26:50,728 nipype.workflow INFO: [Node] Running "bias_correction" ("rabies.preprocess_pkg.bias_correction.EPIBiasCorrection") 201101-07:28:51,526 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bias_correction_wf.bias_correction". 201101-07:28:51,527 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_reg_wf.EPI_Coregistration" in "/outputs/main_wf/bold_main_wf/bold_reg_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/EPI_Coregistration". 201101-07:28:51,576 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_reg_wf.EPI_Coregistration". 201101-07:28:51,645 nipype.workflow INFO: [Node] Running "EPI_Coregistration" ("nipype.interfaces.utility.wrappers.Function") 201101-08:01:01,555 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_reg_wf.EPI_Coregistration". 201101-08:01:01,555 nipype.workflow INFO: [Node] Setting-up "main_wf.transforms_datasink" in "/outputs/main_wf/_scan_info_subjectid3449.session2 split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/transforms_datasink". 201101-08:01:01,680 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.transforms_datasink". 201101-08:01:01,736 nipype.workflow INFO: [Node] Running "transforms_datasink" ("nipype.interfaces.io.DataSink") 201101-08:01:21,663 nipype.workflow INFO: [Node] Finished "main_wf.transforms_datasink". 201101-08:01:21,664 nipype.workflow INFO: [Node] Setting-up "main_wf.PlotOverlap_EPI2Anat" in "/outputs/main_wf/_scan_info_subject_id3449.session2 _split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/PlotOverlap_EPI2Anat". 201101-08:01:21,721 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.PlotOverlap_EPI2Anat". 201101-08:01:21,786 nipype.workflow INFO: [Node] Running "PlotOverlap_EPI2Anat" ("rabies.QC_report.PlotOverlap") 201101-08:01:28,740 nipype.workflow INFO: [Node] Finished "main_wf.PlotOverlap_EPI2Anat". 201101-08:01:28,740 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.commonspace_transforms_prep" in "/outputs/main_wf/bold_mainwf/ scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/commonspace_transforms_prep". 201101-08:01:28,840 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.commonspace_transforms_prep". 201101-08:01:29,166 nipype.workflow INFO: [Node] Running "commonspace_transforms_prep" ("nipype.interfaces.utility.wrappers.Function") 201101-08:01:29,299 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.commonspace_transforms_prep". 201101-08:01:29,300 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_commonspace_trans_wf.bold_transform" in "/outputs/main_wf/b old_main_wf/bold_commonspace_trans_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/ _run_1/bold_transform". 201101-08:01:29,435 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_commonspace_trans_wf.bold_transform". 201101-08:01:31,462 nipype.workflow INFO: [Node] Running "bold_transform" ("rabies.preprocess_pkg.utils.slice_applyTransforms") Splitting bold file into lists of single volumes 201101-10:10:15,227 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_commonspace_trans_wf.bold_transform". 201101-10:10:15,228 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_commonspace_trans_wf.merge" in "/outputs/main_wf/boldmain wf/bold_commonspace_trans_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/me rge". 201101-10:10:35,911 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_commonspace_trans_wf.merge". 201101-10:10:41,924 nipype.workflow INFO: [Node] Running "merge" ("rabies.preprocess_pkg.utils.Merge") 201101-10:13:18,620 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_commonspace_trans_wf.merge". 201101-10:13:18,620 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_commonspace_trans_wf.gen_bold_ref.gen_ref" in "/outputs/mai n_wf/bold_main_wf/bold_commonspace_trans_wf/gen_bold_ref/_scan_info_subject_id3449.session2_split_name_sub-3449_s es-2_acq-FLASH_T1w/_run_1/gen_ref". 201101-10:13:18,655 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_commonspace_trans_wf.gen_bold_ref.gen_ref". 201101-10:13:18,741 nipype.workflow INFO: [Node] Running "gen_ref" ("rabies.preprocess_pkg.utils.EstimateReferenceImage") First iteration to generate reference image. Second iteration to generate reference image. Denoising reference image. 201101-10:15:17,907 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_commonspace_trans_wf.gen_bold_ref.gen_ref". 201101-10:15:17,908 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_commonspace_trans_wf.prop_labels_EPI" in "/outputs/main_wf/ bold_main_wf/bold_commonspace_trans_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w /_run_1/prop_labels_EPI". 201101-10:15:17,982 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_commonspace_trans_wf.prop_labels_EPI". 201101-10:15:18,52 nipype.workflow INFO: [Node] Running "prop_labels_EPI" ("rabies.preprocess_pkg.confounds.MaskEPI") 201101-10:15:18,872 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_commonspace_trans_wf.prop_labels_EPI". 201101-10:15:18,873 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_commonspace_trans_wf.Brain_mask_EPI" in "/outputs/main_wf/b old_main_wf/bold_commonspace_trans_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/ _run_1/Brain_mask_EPI". 201101-10:15:18,920 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_commonspace_trans_wf.Brain_mask_EPI". 201101-10:15:18,970 nipype.workflow INFO: [Node] Running "Brain_mask_EPI" ("rabies.preprocess_pkg.confounds.MaskEPI") 201101-10:15:19,278 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_commonspace_trans_wf.Brain_mask_EPI". 201101-10:15:19,279 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_commonspace_trans_wf.vascular_mask_EPI" in "/outputs/main_w f/bold_main_wf/bold_commonspace_trans_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T 1w/_run_1/vascular_mask_EPI". 201101-10:15:19,322 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_commonspace_trans_wf.vascular_mask_EPI". 201101-10:15:19,371 nipype.workflow INFO: [Node] Running "vascular_mask_EPI" ("rabies.preprocess_pkg.confounds.MaskEPI") 201101-10:15:19,601 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_commonspace_trans_wf.vascular_mask_EPI". 201101-10:15:19,601 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_commonspace_trans_wf.CSF_mask_EPI" in "/outputs/main_wf/bol d_main_wf/bold_commonspace_trans_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_r un_1/CSF_mask_EPI". 201101-10:15:19,645 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_commonspace_trans_wf.CSF_mask_EPI". 201101-10:15:19,694 nipype.workflow INFO: [Node] Running "CSF_mask_EPI" ("rabies.preprocess_pkg.confounds.MaskEPI") 201101-10:15:26,420 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_commonspace_trans_wf.CSF_mask_EPI". 201101-10:15:26,421 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_commonspace_trans_wf.WM_mask_EPI" in "/outputs/main_wf/bold _main_wf/bold_commonspace_trans_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_ru n_1/WM_mask_EPI". 201101-10:15:26,465 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_commonspace_trans_wf.WM_mask_EPI". 201101-10:15:26,514 nipype.workflow INFO: [Node] Running "WM_mask_EPI" ("rabies.preprocess_pkg.confounds.MaskEPI") 201101-10:15:33,243 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_commonspace_trans_wf.WM_mask_EPI". 201101-10:15:33,243 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.transforms_prep" in "/outputs/main_wf/bold_main_wf/_scan_info_su bject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/transforms_prep". 201101-10:15:33,282 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.transforms_prep". 201101-10:15:33,321 nipype.workflow INFO: [Node] Running "transforms_prep" ("nipype.interfaces.utility.wrappers.Function") 201101-10:15:33,402 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.transforms_prep". 201101-10:15:33,403 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_native_trans_wf.bold_transform" in "/outputs/main_wf/bold_m ain_wf/bold_native_trans_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/bol d_transform". 201101-10:15:33,501 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_native_trans_wf.bold_transform". 201101-10:15:35,385 nipype.workflow INFO: [Node] Running "bold_transform" ("rabies.preprocess_pkg.utils.slice_applyTransforms") Splitting bold file into lists of single volumes 201101-11:45:34,974 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_native_trans_wf.bold_transform". 201101-11:45:34,974 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_native_trans_wf.merge" in "/outputs/main_wf/bold_main_wf/bold_native_trans_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/merge". 201101-11:45:56,179 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_native_trans_wf.merge". 201101-11:46:02,309 nipype.workflow INFO: [Node] Running "merge" ("rabies.preprocess_pkg.utils.Merge") 201101-11:50:28,697 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_native_trans_wf.merge". 201101-11:50:28,698 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_native_trans_wf.gen_bold_ref.gen_ref" in "/outputs/main_wf/bold_main_wf/bold_native_trans_wf/gen_bold_ref/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/gen_ref". 201101-11:50:28,736 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_native_trans_wf.gen_bold_ref.gen_ref". 201101-11:50:28,813 nipype.workflow INFO: [Node] Running "gen_ref" ("rabies.preprocess_pkg.utils.EstimateReferenceImage") First iteration to generate reference image. Second iteration to generate reference image. Denoising reference image. 201101-11:53:43,394 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_native_trans_wf.gen_bold_ref.gen_ref". 201101-11:53:43,395 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_confs_wf.prop_labels_EPI" in "/outputs/main_wf/bold_main_wf/bold_confs_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/prop_labels_EPI". 201101-11:53:43,457 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_confs_wf.prop_labels_EPI". 201101-11:53:43,526 nipype.workflow INFO: [Node] Running "prop_labels_EPI" ("rabies.preprocess_pkg.confounds.MaskEPI") 201101-11:53:44,426 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_confs_wf.prop_labels_EPI". 201101-11:53:44,427 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_confs_wf.Brain_mask_EPI" in "/outputs/main_wf/bold_main_wf/bold_confs_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/Brain_mask_EPI". 201101-11:53:44,485 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_confs_wf.Brain_mask_EPI". 201101-11:53:44,554 nipype.workflow INFO: [Node] Running "Brain_mask_EPI" ("rabies.preprocess_pkg.confounds.MaskEPI") 201101-11:53:45,84 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_confs_wf.Brain_mask_EPI". 201101-11:53:45,84 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_confs_wf.vascular_mask_EPI" in "/outputs/main_wf/bold_main_wf/bold_confs_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/vascular_mask_EPI". 201101-11:53:45,142 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_confs_wf.vascular_mask_EPI". 201101-11:53:45,195 nipype.workflow INFO: [Node] Running "vascular_mask_EPI" ("rabies.preprocess_pkg.confounds.MaskEPI") 201101-11:53:45,724 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_confs_wf.vascular_mask_EPI". 201101-11:53:45,724 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_confs_wf.CSF_mask_EPI" in "/outputs/main_wf/bold_main_wf/bold_confs_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/CSF_mask_EPI". 201101-11:53:45,782 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_confs_wf.CSF_mask_EPI". 201101-11:53:45,835 nipype.workflow INFO: [Node] Running "CSF_mask_EPI" ("rabies.preprocess_pkg.confounds.MaskEPI") 201101-11:54:00,960 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_confs_wf.CSF_mask_EPI". 201101-11:54:00,961 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_confs_wf.WM_mask_EPI" in "/outputs/main_wf/bold_main_wf/bold_confs_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/WM_mask_EPI". 201101-11:54:01,20 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_confs_wf.WM_mask_EPI". 201101-11:54:01,75 nipype.workflow INFO: [Node] Running "WM_mask_EPI" ("rabies.preprocess_pkg.confounds.MaskEPI") 201101-11:54:15,462 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_confs_wf.WM_mask_EPI". 201101-11:54:15,462 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_datasink" in "/outputs/main_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/bold_datasink". 201101-11:54:15,741 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_datasink". 201101-11:54:15,796 nipype.workflow INFO: [Node] Running "bold_datasink" ("nipype.interfaces.io.DataSink") 201101-11:56:20,222 nipype.workflow INFO: [Node] Finished "main_wf.bold_datasink". 201101-11:56:20,223 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_confs_wf.estimate_confounds" in "/outputs/main_wf/bold_main_wf/bold_confs_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/estimate_confounds". 201101-11:56:20,347 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_confs_wf.estimate_confounds". 201101-11:56:20,431 nipype.workflow INFO: [Node] Running "estimate_confounds" ("rabies.preprocess_pkg.confounds.EstimateConfounds") Extracting 4 components for aCompCorr. 201101-12:11:31,130 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_confs_wf.estimate_confounds". 201101-12:11:31,131 nipype.workflow INFO: [Node] Setting-up "main_wf.confounds_datasink" in "/outputs/main_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/confounds_datasink". 201101-12:11:31,155 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.confounds_datasink". 201101-12:11:31,191 nipype.workflow INFO: [Node] Running "confounds_datasink" ("nipype.interfaces.io.DataSink") 201101-12:12:07,488 nipype.workflow INFO: [Node] Finished "main_wf.confounds_datasink". 201101-12:12:07,489 nipype.workflow INFO: [Node] Setting-up "main_wf.PlotMotionTrace" in "/outputs/main_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/_run_1/PlotMotionTrace". 201101-12:12:07,509 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.PlotMotionTrace". 201101-12:12:07,543 nipype.workflow INFO: [Node] Running "PlotMotionTrace" ("rabies.QC_report.PlotMotionTrace") 201101-12:12:08,100 nipype.workflow INFO: [Node] Finished "main_wf.PlotMotionTrace". 201101-12:12:08,101 nipype.workflow INFO: [Node] Setting-up "main_wf.anat_datasink" in "/outputs/main_wf/_scan_info_subject_id3449.session2_split_name_sub-3449_ses-2_acq-FLASH_T1w/anat_datasink". 201101-12:12:08,149 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.anat_datasink". 201101-12:12:08,179 nipype.workflow INFO: [Node] Running "anat_datasink" ("nipype.interfaces.io.DataSink") 201101-12:12:10,155 nipype.workflow INFO: [Node] Finished "main_wf.anat_datasink". 201101-12:12:10,156 nipype.workflow INFO: [Node] Setting-up "main_wf.transform_masks" in "/outputs/main_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/transform_masks". 201101-12:12:10,217 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.transform_masks". 201101-12:12:10,281 nipype.workflow INFO: [Node] Running "transform_masks" ("nipype.interfaces.utility.wrappers.Function") 201101-12:19:13,583 nipype.workflow INFO: [Node] Finished "main_wf.transform_masks". 201101-12:19:13,583 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bias_correction_wf.bias_correction" in "/outputs/main_wf/bold_main_wf/bias_correction_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/bias_correction". 201101-12:19:13,641 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bias_correction_wf.bias_correction". 201101-12:19:13,694 nipype.workflow INFO: [Node] Running "bias_correction" ("rabies.preprocess_pkg.bias_correction.EPIBiasCorrection") 201101-12:21:05,668 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bias_correction_wf.bias_correction". 201101-12:21:05,669 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_reg_wf.EPI_Coregistration" in "/outputs/main_wf/bold_main_wf/bold_reg_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/EPI_Coregistration". 201101-12:21:05,707 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_reg_wf.EPI_Coregistration". 201101-12:21:05,767 nipype.workflow INFO: [Node] Running "EPI_Coregistration" ("nipype.interfaces.utility.wrappers.Function") 201101-12:52:48,650 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_reg_wf.EPI_Coregistration". 201101-12:52:48,651 nipype.workflow INFO: [Node] Setting-up "main_wf.transforms_datasink" in "/outputs/main_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/transforms_datasink". 201101-12:52:48,756 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.transforms_datasink". 201101-12:52:48,793 nipype.workflow INFO: [Node] Running "transforms_datasink" ("nipype.interfaces.io.DataSink") 201101-12:53:01,717 nipype.workflow INFO: [Node] Finished "main_wf.transforms_datasink". 201101-12:53:01,718 nipype.workflow INFO: [Node] Setting-up "main_wf.PlotOverlap_EPI2Anat" in "/outputs/main_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/PlotOverlap_EPI2Anat". 201101-12:53:01,763 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.PlotOverlap_EPI2Anat". 201101-12:53:01,796 nipype.workflow INFO: [Node] Running "PlotOverlap_EPI2Anat" ("rabies.QC_report.PlotOverlap") 201101-12:53:08,605 nipype.workflow INFO: [Node] Finished "main_wf.PlotOverlap_EPI2Anat". 201101-12:53:08,606 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.commonspace_transforms_prep" in "/outputs/main_wf/bold_main_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/commonspace_transforms_prep". 201101-12:53:08,670 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.commonspace_transforms_prep". 201101-12:53:08,703 nipype.workflow INFO: [Node] Running "commonspace_transforms_prep" ("nipype.interfaces.utility.wrappers.Function") 201101-12:53:08,798 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.commonspace_transforms_prep". 201101-12:53:08,798 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_commonspace_trans_wf.bold_transform" in "/outputs/main_wf/bold_main_wf/bold_commonspace_trans_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/bold_transform". 201101-12:53:08,896 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_commonspace_trans_wf.bold_transform". 201101-12:53:10,713 nipype.workflow INFO: [Node] Running "bold_transform" ("rabies.preprocess_pkg.utils.slice_applyTransforms") Splitting bold file into lists of single volumes 201101-15:03:03,236 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_commonspace_trans_wf.bold_transform". 201101-15:03:03,237 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_commonspace_trans_wf.merge" in "/outputs/main_wf/bold_main_wf/bold_commonspace_trans_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/merge". 201101-15:03:18,409 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_commonspace_trans_wf.merge". 201101-15:03:22,921 nipype.workflow INFO: [Node] Running "merge" ("rabies.preprocess_pkg.utils.Merge") 201101-15:06:00,560 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_commonspace_trans_wf.merge". 201101-15:06:00,560 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_commonspace_trans_wf.gen_bold_ref.gen_ref" in "/outputs/main_wf/bold_main_wf/bold_commonspace_trans_wf/gen_bold_ref/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/gen_ref". 201101-15:06:00,586 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_commonspace_trans_wf.gen_bold_ref.gen_ref". 201101-15:06:00,666 nipype.workflow INFO: [Node] Running "gen_ref" ("rabies.preprocess_pkg.utils.EstimateReferenceImage") First iteration to generate reference image. Second iteration to generate reference image. Denoising reference image. 201101-15:07:47,303 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_commonspace_trans_wf.gen_bold_ref.gen_ref". 201101-15:07:47,304 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_commonspace_trans_wf.prop_labels_EPI" in "/outputs/main_wf/bold_main_wf/bold_commonspace_trans_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/prop_labels_EPI". 201101-15:07:47,347 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_commonspace_trans_wf.prop_labels_EPI". 201101-15:07:47,393 nipype.workflow INFO: [Node] Running "prop_labels_EPI" ("rabies.preprocess_pkg.confounds.MaskEPI") 201101-15:07:48,180 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_commonspace_trans_wf.prop_labels_EPI". 201101-15:07:48,181 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_commonspace_trans_wf.Brain_mask_EPI" in "/outputs/main_wf/bold_main_wf/bold_commonspace_trans_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/Brain_mask_EPI". 201101-15:07:48,223 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_commonspace_trans_wf.Brain_mask_EPI". 201101-15:07:48,286 nipype.workflow INFO: [Node] Running "Brain_mask_EPI" ("rabies.preprocess_pkg.confounds.MaskEPI") 201101-15:07:48,587 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_commonspace_trans_wf.Brain_mask_EPI". 201101-15:07:48,587 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_commonspace_trans_wf.vascular_mask_EPI" in "/outputs/main_wf/bold_main_wf/bold_commonspace_trans_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/vascular_mask_EPI". 201101-15:07:48,622 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_commonspace_trans_wf.vascular_mask_EPI". 201101-15:07:48,663 nipype.workflow INFO: [Node] Running "vascular_mask_EPI" ("rabies.preprocess_pkg.confounds.MaskEPI") 201101-15:07:48,876 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_commonspace_trans_wf.vascular_mask_EPI". 201101-15:07:48,877 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_commonspace_trans_wf.CSF_mask_EPI" in "/outputs/main_wf/bold_main_wf/bold_commonspace_trans_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/CSF_mask_EPI". 201101-15:07:48,912 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_commonspace_trans_wf.CSF_mask_EPI". 201101-15:07:48,953 nipype.workflow INFO: [Node] Running "CSF_mask_EPI" ("rabies.preprocess_pkg.confounds.MaskEPI") 201101-15:07:55,659 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_commonspace_trans_wf.CSF_mask_EPI". 201101-15:07:55,659 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_commonspace_trans_wf.WM_mask_EPI" in "/outputs/main_wf/bold_main_wf/bold_commonspace_trans_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/WM_mask_EPI". 201101-15:07:55,695 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_commonspace_trans_wf.WM_mask_EPI". 201101-15:07:55,737 nipype.workflow INFO: [Node] Running "WM_mask_EPI" ("rabies.preprocess_pkg.confounds.MaskEPI") 201101-15:08:02,839 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_commonspace_trans_wf.WM_mask_EPI". 201101-15:08:02,840 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.transforms_prep" in "/outputs/main_wf/bold_main_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/transforms_prep". 201101-15:08:02,868 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.transforms_prep". 201101-15:08:02,899 nipype.workflow INFO: [Node] Running "transforms_prep" ("nipype.interfaces.utility.wrappers.Function") 201101-15:08:02,963 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.transforms_prep". 201101-15:08:02,963 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_native_trans_wf.bold_transform" in "/outputs/main_wf/bold_main_wf/bold_native_trans_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/bold_transform". 201101-15:08:03,39 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_native_trans_wf.bold_transform". 201101-15:08:04,843 nipype.workflow INFO: [Node] Running "bold_transform" ("rabies.preprocess_pkg.utils.slice_applyTransforms") Splitting bold file into lists of single volumes 201101-16:42:35,531 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_native_trans_wf.bold_transform". 201101-16:42:35,532 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_native_trans_wf.merge" in "/outputs/main_wf/bold_main_wf/bold_native_trans_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/merge". 201101-16:42:50,903 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_native_trans_wf.merge". 201101-16:42:55,370 nipype.workflow INFO: [Node] Running "merge" ("rabies.preprocess_pkg.utils.Merge") 201101-16:47:19,857 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_native_trans_wf.merge". 201101-16:47:19,857 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_native_trans_wf.gen_bold_ref.gen_ref" in "/outputs/main_wf/bold_main_wf/bold_native_trans_wf/gen_bold_ref/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/gen_ref". 201101-16:47:19,885 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_native_trans_wf.gen_bold_ref.gen_ref". 201101-16:47:19,949 nipype.workflow INFO: [Node] Running "gen_ref" ("rabies.preprocess_pkg.utils.EstimateReferenceImage") First iteration to generate reference image. Second iteration to generate reference image. Denoising reference image. 201101-16:50:22,393 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_native_trans_wf.gen_bold_ref.gen_ref". 201101-16:50:22,394 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_confs_wf.prop_labels_EPI" in "/outputs/main_wf/bold_main_wf/bold_confs_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/prop_labels_EPI". 201101-16:50:22,443 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_confs_wf.prop_labels_EPI". 201101-16:50:22,485 nipype.workflow INFO: [Node] Running "prop_labels_EPI" ("rabies.preprocess_pkg.confounds.MaskEPI") 201101-16:50:23,479 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_confs_wf.prop_labels_EPI". 201101-16:50:23,479 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_confs_wf.Brain_mask_EPI" in "/outputs/main_wf/bold_main_wf/bold_confs_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/Brain_mask_EPI". 201101-16:50:23,527 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_confs_wf.Brain_mask_EPI". 201101-16:50:23,564 nipype.workflow INFO: [Node] Running "Brain_mask_EPI" ("rabies.preprocess_pkg.confounds.MaskEPI") 201101-16:50:24,70 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_confs_wf.Brain_mask_EPI". 201101-16:50:24,71 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_confs_wf.vascular_mask_EPI" in "/outputs/main_wf/bold_main_wf/bold_confs_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/vascular_mask_EPI". 201101-16:50:24,119 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_confs_wf.vascular_mask_EPI". 201101-16:50:24,155 nipype.workflow INFO: [Node] Running "vascular_mask_EPI" ("rabies.preprocess_pkg.confounds.MaskEPI") 201101-16:50:24,656 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_confs_wf.vascular_mask_EPI". 201101-16:50:24,657 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_confs_wf.CSF_mask_EPI" in "/outputs/main_wf/bold_main_wf/bold_confs_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/CSF_mask_EPI". 201101-16:50:24,706 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_confs_wf.CSF_mask_EPI". 201101-16:50:24,742 nipype.workflow INFO: [Node] Running "CSF_mask_EPI" ("rabies.preprocess_pkg.confounds.MaskEPI") 201101-16:50:38,664 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_confs_wf.CSF_mask_EPI". 201101-16:50:38,665 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_confs_wf.WM_mask_EPI" in "/outputs/main_wf/bold_main_wf/bold_confs_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/WM_mask_EPI". 201101-16:50:38,713 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_main_wf.bold_confs_wf.WM_mask_EPI". 201101-16:50:38,750 nipype.workflow INFO: [Node] Running "WM_mask_EPI" ("rabies.preprocess_pkg.confounds.MaskEPI") 201101-16:50:52,360 nipype.workflow INFO: [Node] Finished "main_wf.bold_main_wf.bold_confs_wf.WM_mask_EPI". 201101-16:50:52,361 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_datasink" in "/outputs/main_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/bold_datasink". 201101-16:50:52,571 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.bold_datasink". 201101-16:50:52,625 nipype.workflow INFO: [Node] Running "bold_datasink" ("nipype.interfaces.io.DataSink") 201101-16:52:53,632 nipype.workflow INFO: [Node] Finished "main_wf.bold_datasink". 201101-16:52:53,633 nipype.workflow INFO: [Node] Setting-up "main_wf.bold_main_wf.bold_confs_wf.estimate_confounds" in "/outputs/main_wf/bold_main_wf/bold_confs_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/estimate_confounds". 201101-16:52:53,779 nipype.workflow INFO: [Node] Running "estimate_confounds" ("rabies.preprocess_pkg.confounds.EstimateConfounds") 201101-17:02:35,340 nipype.workflow WARNING: [Node] Error on "main_wf.bold_main_wf.bold_confs_wf.estimate_confounds" (/outputs/main_wf/bold_main_wf/bold_confs_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1/estimate_confounds) 201101-17:02:35,363 nipype.workflow ERROR: Node estimate_confounds.a0.a0 failed to run on host 36a479d23bbf. 201101-17:02:35,364 nipype.workflow ERROR: Saving crash info to /tmp/crash-20201101-170235-root-estimate_confounds.a0.a0-67c5a75c-8c4c-4058-94b5-01797fb9bd99.pklz Traceback (most recent call last): File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run node.run(updatehash=updatehash) File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run result = self._run_interface(execute=True) File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface return self._run_command(execute) File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command result = self._interface.run(cwd=outdir) File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 522, in run runtime = self._run_interface(runtime) File "/home/rabies/RABIES-0.2.0/rabies/preprocess_pkg/confounds.py", line 150, in _run_interface WM_signal = extract_mask_trace(self.inputs.bold, self.inputs.WM_mask) File "/home/rabies/RABIES-0.2.0/rabies/preprocess_pkg/confounds.py", line 290, in extract_mask_trace mask_signal = nilearn.masking.apply_mask(bold, mask) File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nilearn/masking.py", line 702, in apply_mask mask, mask_affine = _load_mask_img(mask_img) File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nilearn/masking.py", line 52, in _load_mask_img 'The mask is invalid as it is empty: it masks all data.') ValueError: The mask is invalid as it is empty: it masks all data. 201101-17:02:35,387 nipype.workflow INFO: [Node] Setting-up "main_wf.anat_datasink" in "/outputs/main_wf/_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/anat_datasink". 201101-17:02:35,437 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.anat_datasink". 201101-17:02:35,483 nipype.workflow INFO: [Node] Running "anat_datasink" ("nipype.interfaces.io.DataSink") 201101-17:02:38,500 nipype.workflow INFO: [Node] Finished "main_wf.anat_datasink". 201101-17:02:38,500 nipype.workflow INFO: [Node] Setting-up "main_wf.commonspace_datasink" in "/outputs/main_wf/commonspace_datasink". 201101-17:02:38,525 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.commonspace_datasink". 201101-17:02:38,551 nipype.workflow INFO: [Node] Running "commonspace_datasink" ("nipype.interfaces.io.DataSink") 201101-17:02:39,215 nipype.workflow INFO: [Node] Finished "main_wf.commonspace_datasink". 201101-17:02:39,216 nipype.workflow INFO: [Node] Setting-up "main_wf.PlotOverlap_Template2Commonspace" in "/outputs/main_wf/PlotOverlap_Template2Commonspace". 201101-17:02:39,234 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.PlotOverlap_Template2Commonspace". 201101-17:02:39,260 nipype.workflow INFO: [Node] Running "PlotOverlap_Template2Commonspace" ("rabies.QC_report.PlotOverlap") 201101-17:02:43,736 nipype.workflow INFO: [Node] Finished "main_wf.PlotOverlap_Template2Commonspace". 201101-17:02:43,736 nipype.workflow INFO:

201101-17:02:43,736 nipype.workflow ERROR: could not run node: main_wf.bold_main_wf.bold_confs_wf.estimate_confounds.a0.a0 201101-17:02:43,737 nipype.workflow INFO: crashfile: /tmp/crash-20201101-170235-root-estimate_confounds.a0.a0-67c5a75c-8c4c-4058-94b5-01797fb9bd99.pklz 201101-17:02:43,737 nipype.workflow INFO:

Traceback (most recent call last): File "/home/rabies/RABIES-0.2.0/exec.py", line 13, in execute_workflow() File "/home/rabies/RABIES-0.2.0/rabies/run_main.py", line 315, in execute_workflow 'n_procs': opts.local_threads, 'qsub_args': '-pe smp %s' % (str(opts.min_proc))}) File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nipype/pipeline/engine/workflows.py", line 595, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 61, in run report_nodes_not_run(notrun) File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nipype/pipeline/plugins/tools.py", line 82, in report_nodes_not_run raise RuntimeError(('Workflow did not execute cleanly. ' RuntimeError: Workflow did not execute cleanly. Check log for details

ChristianNSchmitz commented 3 years ago

Running it on debugging mode results in this error:

... [Node] Running "resample_template" ("nipype.interfaces.utility.wrappers.Function") Resampling template to 0.15003332495689392x0.15003332495689392x0.15003332495689392mm dimensions. 201102-09:48:45,175 nipype.workflow INFO: [Node] Finished "main_wf.resample_template". 201102-09:48:45,176 nipype.workflow INFO: [Node] Setting-up "main_wf.anat_preproc_wf.Anat_Preproc" in "/outputs/main_wf/anat_preproc_wf/_scan_info_subject_id3449.session2_spli 201102-09:48:45,207 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.anat_preproc_wf.Anat_Preproc". 201102-09:48:45,259 nipype.workflow INFO: [Node] Running "Anat_Preproc" ("rabies.preprocess_pkg.anat_preproc.AnatPreproc") Anat image will be resampled to the template resolution. 201102-09:56:26,818 nipype.workflow INFO: [Node] Finished "main_wf.anat_preproc_wf.Anat_Preproc". 201102-09:56:26,819 nipype.workflow INFO: [Node] Setting-up "main_wf.anat_preproc_wf.Anat_Preproc" in "/outputs/main_wf/anat_preproc_wf/_scan_info_subject_id3449.session1_spli 201102-09:56:26,849 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.anat_preproc_wf.Anat_Preproc". 201102-09:56:26,909 nipype.workflow INFO: [Node] Running "Anat_Preproc" ("rabies.preprocess_pkg.anat_preproc.AnatPreproc") Anat image will be resampled to the template resolution. 201102-10:04:32,465 nipype.workflow INFO: [Node] Finished "main_wf.anat_preproc_wf.Anat_Preproc". 201102-10:04:32,466 nipype.workflow INFO: [Node] Setting-up "main_wf.commonspace_reg" in "/outputs/main_wf/commonspace_reg". 201102-10:04:32,507 nipype.workflow INFO: [Node] Outdated cache found for "main_wf.commonspace_reg". 201102-10:04:32,549 nipype.workflow INFO: [Node] Running "commonspace_reg" ("rabies.preprocess_pkg.commonspace.ANTsDBM") Previous ants_dbm_outputs/ folder detected. Inputs from a previous run may cause issues for the commonspace registration, so consider removing Running the following commonspace registration: twolevel_dbm.py --rigid-model-target /outputs/main_wf/resample_template/resampled_template.nii.gz --no-N4 --transform SyN --float --average-tyIES-0.2.0/rabies/shell_scripts/antsMultivariateTemplateConstruction2.sh --cluster-type local --walltime 20:00:00 --memory-request 1gb --local- 100%|##########| 2/2 [00:00<00:00, 297.75it/s] 0%| | 0/6 [00:00<?, ?it/s]twolevel_dbm.py: Processing Second-Level DBM outputs twolevel_dbm.py: Blurring Jacobians Traceback (most recent call last): File "/home/rabies/RABIES-0.2.0/twolevel_ants_dbm/twolevel_dbm.py", line 860, in main() File "/home/rabies/RABIES-0.2.0/twolevel_ants_dbm/twolevel_dbm.py", line 856, in main secondlevel(inputs, args, secondlevel=False) File "/home/rabies/RABIES-0.2.0/twolevel_ants_dbm/twolevel_dbm.py", line 636, in secondlevel total=len(commands), File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/tqdm/_tqdm.py", line 1005, in iter for obj in iterable: File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/multiprocess/pool.py", line 735, in next raise value File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/multiprocess/pool.py", line 119, in worker result = (True, func(*args, *kwds)) File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/pathos/helpers/mp_helper.py", line 15, in func = lambda args: f(args) File "/home/rabies/RABIES-0.2.0/twolevel_ants_dbm/twolevel_dbm.py", line 635, in pool.uimap(lambda x: run_command(x, args.dry_run, args.verbose), commands), File "/home/rabies/RABIES-0.2.0/twolevel_ants_dbm/twolevel_dbm.py", line 35, in run_command shell=True, File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/subprocess.py", line 438, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command 'SmoothImage 3 output/jacobians/overall/secondlevel_sub-3449_ses-1_acq-FLASH_T1w_RAS_preproc_relative.n_RAS_preproc_relative_smooth0.12742629766261238.nii.gz 1 0' returned non-zero exit status 134. 201102-10:04:33,998 nipype.workflow WARNING: [Node] Error on "main_wf.commonspace_reg" (/outputs/main_wf/commonspace_reg) Traceback (most recent call last): File "/home/rabies/RABIES-0.2.0/exec.py", line 13, in execute_workflow() File "/home/rabies/RABIES-0.2.0/rabies/run_main.py", line 315, in execute_workflow 'n_procs': opts.local_threads, 'qsub_args': '-pe smp %s' % (str(opts.min_proc))}) File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nipype/pipeline/engine/workflows.py", line 595, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run node.run(updatehash=updatehash) File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run result = self._run_interface(execute=True) File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface return self._run_command(execute) File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 880, in _run_command return super(JoinNode, self)._run_command(execute, copyfiles) File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command result = self._interface.run(cwd=outdir) File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 522, in run runtime = self._run_interface(runtime) File "/home/rabies/RABIES-0.2.0/rabies/preprocess_pkg/commonspace.py", line 131, in _run_interface anat_to_template_inverse_warp+" file doesn't exists.") ValueError: /outputs/commonspace_datasink//ants_dbm_outputs//output/secondlevel/secondlevel_sub-3449_ses-1_acq-FLASH_T1w_RAS_preproc01InverseW

Gab-D-G commented 3 years ago

Hi Christian, I am not sure what was the original error with the confound regression step, I haven't encountered this one before. I believe an error resulted in the debug mode by re-running the debug in the same folder which had a previous commonspace registration as specified from 'Previous ants_dbm_outputs/ folder detected. Inputs from a previous run may cause issues for the commonspace registration, so consider removing'. So I would suggest re-running in a new folder, or at least remove the commonspace registration datasink folder, and main_bold/commonspace_reg before re-running in debug mode. You could take a look at whether the registration of the scan '_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1' has worked, because the error might arise from a complete registration failure where the mask is not overlapping with the image. Also, make sure that the mask you provided is appropriately overlapping with the original template, in case.

I hope this helps! Best, Gabe

ChristianNSchmitz commented 3 years ago

Dear Gabe,

thanks for the quick reply! I have checked both the overlapping of the mask with the original template, the registration of the scan '_scan_info_subject_id3449.session1_split_name_sub-3449_ses-1_acq-FLASH_T1w/_run_1' and I have already removed all output directories. However, the issue remains and I would like to ask you whether there is any other option.

Thanks a lot! Best, Christian

gdevenyi commented 3 years ago

Can you post the complete run log please.

ChristianNSchmitz commented 3 years ago

rabies_preprocess.log

Sure, you can find it attached.

ChristianNSchmitz commented 3 years ago

Dear Gabe, dear gdevenyi,

thanks for your help, I was able to resolve the issue. The issue was related to wrong read-write permission.

Running the analysis on a single animal worked. However, I have some issues running it for several subjects simultaneously. You can find the terminal output and the log file attached. Thanks a lot for your help!

Best, Christian rabies_preprocess_Log.log terminal.txt

gdevenyi commented 3 years ago

Hi,

Since the processing is based on your BIDS structure, can you please also provide output of tree or find on the BIDS dataset, and the contents of the subject details files.

@Gab-D-G this is the repeated python failure, my guess is the BIDS structure is getting misread or is malformed?

Traceback (most recent call last):
  File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py",
    node.run(updatehash=updatehash)
  File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", l
    result = self._run_interface(execute=True)
  File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", l
    return self._run_command(execute)
  File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", l
    result = self._interface.run(cwd=outdir)
  File "/home/rabies/miniconda-latest/envs/rabies/lib/python3.6/site-packages/nipype/interfaces/base/core.py", li
    runtime = self._run_interface(runtime)
  File "/home/rabies/RABIES-0.2.0/rabies/preprocess_pkg/utils.py", line 144, in _run_interface
    setattr(self, 'out_file', file_list[0])
IndexError: list index out of range
ChristianNSchmitz commented 3 years ago

Sure:

/mnt/d/PsiAlc/RabiesDir# tree rawdata

rawdata
├── README
├── dataset_description.json
├── sub-3449
│   ├── ses-1
│   │   ├── anat
│   │   │   └── sub-3449_ses-1_run-01_T2w.nii
│   │   └── func
│   │       └── sub-3449_ses-1_run-01_task-rest_bold.nii
│   └── ses-2
│       ├── anat
│       │   └── sub-3449_ses-2_run-01_T2w.nii
│       └── func
│           └── sub-3449_ses-2_run-01_task-rest_bold.nii
├── sub-3452
│   ├── ses-1
│   │   ├── anat
│   │   │   └── sub-3452_ses-1_run-01_T2w.nii
│   │   └── func
│   │       └── sub-3452_ses-1_run-01_task-rest_bold.nii
│   └── ses-2
│       ├── anat
│       │   └── sub-3452_ses-2_run-01_T2w.nii
│       └── func
│           └── sub-3452_ses-2_run-01_task-rest_bold.nii
├── sub-3454
│   ├── ses-1
│   │   ├── anat
│   │   │   └── sub-3454_ses-1_run-01_T2w.nii
│   │   └── func
│   │       └── sub-3454_ses-1_run-01_task-rest_bold.nii
│   └── ses-2
│       ├── anat
│       │   └── sub-3454_ses-2_run-01_T2w.nii
│       └── func
│           └── sub-3454_ses-2_run-01_task-rest_bold.nii
├── sub-3461
│   ├── ses-1
│   │   ├── anat
│   │   │   └── sub-3461_ses-1_run-01_T2w.nii
│   │   └── func
│   │       └── sub-3461_ses-1_run-01_task-rest_bold.nii
│   └── ses-2
│       ├── anat
│       │   └── sub-3461_ses-2_run-01_T2w.nii
│       └── func
│           └── sub-3461_ses-2_run-01_task-rest_bold.nii
├── sub-3470
│   ├── ses-1
│   │   ├── anat
│   │   │   └── sub-3470_ses-1_run-01_T2w.nii
│   │   └── func
│   │       └── sub-3470_ses-1_run-01_task-rest_bold.nii
│   └── ses-2
│       ├── anat
│       │   └── sub-3470_ses-2_run-01_T2w.nii
│       └── func
│           └── sub-3470_ses-2_run-01_task-rest_bold.nii
├── sub-3472
│   ├── ses-1
│   │   ├── anat
│   │   │   └── sub-3472_ses-1_run-01_T2w.nii
│   │   └── func
│   │       └── sub-3472_ses-1_run-01_task-rest_bold.nii
│   └── ses-2
│       ├── anat
│       │   └── sub-3472_ses-2_run-01_T2w.nii
│       └── func
│           └── sub-3472_ses-2_run-01_task-rest_bold.nii
├── sub-3484
│   └── ses-2
│       ├── anat
│       │   └── sub-3484_ses-2_run-01_T2w.nii
│       └── func
│           └── sub-3484_ses-2_run-01_task-rest_bold.nii
├── sub-3485
│   └── ses-2
│       ├── anat
│       │   └── sub-3485_ses-2_run-01_T2w.nii
│       └── func
│           └── sub-3485_ses-2_run-01_task-rest_bold.nii
├── sub-3488
│   ├── ses-1
│   │   ├── anat
│   │   │   └── sub-3488_ses-1_run-01_T2w.nii
│   │   └── func
│   │       └── sub-3488_ses-1_run-01_task-rest_bold.nii
│   └── ses-2
│       ├── anat
│       │   └── sub-3488_ses-2_run-01_T2w.nii
│       └── func
│           └── sub-3488_ses-2_run-01_task-rest_bold.nii
├── sub-3492
│   └── ses-2
│       ├── anat
│       │   └── sub-3492_ses-2_run-01_T2w.nii
│       └── func
│           └── sub-3492_ses-2_run-01_task-rest_bold.nii
├── sub-3493
│   ├── ses-1
│   │   ├── anat
│   │   │   └── sub-3493_ses-1_run-01_T2w.nii
│   │   └── func
│   │       └── sub-3493_ses-1_run-01_task-rest_bold.nii
│   └── ses-2
│       ├── anat
│       │   └── sub-3493_ses-2_run-01_T2w.nii
│       └── func
│           └── sub-3493_ses-2_run-01_task-rest_bold.nii
├── sub-3496
│   └── ses-2
│       ├── anat
│       │   └── sub-3496_ses-2_run-01_T2w.nii
│       └── func
│           └── sub-3496_ses-2_run-01_task-rest_bold.nii
├── sub-3511
│   ├── ses-1
│   │   ├── anat
│   │   │   └── sub-3511_ses-1_run-01_T2w.nii
│   │   └── func
│   │       └── sub-3511_ses-1_run-01_task-rest_bold.nii
│   └── ses-2
│       ├── anat
│       │   └── sub-3511_ses-2_run-01_T2w.nii
│       └── func
│           └── sub-3511_ses-2_run-01_task-rest_bold.nii
├── sub-3531
│   ├── ses-1
│   │   ├── anat
│   │   │   └── sub-3531_ses-1_run-01_T2w.nii
│   │   └── func
│   │       └── sub-3531_ses-1_run-01_task-rest_bold.nii
│   └── ses-2
│       ├── anat
│       │   └── sub-3531_ses-2_run-01_T2w.nii
│       └── func
│           └── sub-3531_ses-2_run-01_task-rest_bold.nii
├── sub-3532
│   ├── ses-1
│   │   ├── anat
│   │   │   └── sub-3532_ses-1_run-01_T2w.nii
│   │   └── func
│   │       └── sub-3532_ses-1_run-01_task-rest_bold.nii
│   └── ses-2
│       ├── anat
│       │   └── sub-3532_ses-2_run-01_T2w.nii
│       └── func
│           └── sub-3532_ses-2_run-01_task-rest_bold.nii
├── sub-3538
│   ├── ses-1
│   │   ├── anat
│   │   │   └── sub-3538_ses-1_run-01_T2w.nii
│   │   └── func
│   │       └── sub-3538_ses-1_run-01_task-rest_bold.nii
│   └── ses-2
│       ├── anat
│       │   └── sub-3538_ses-2_run-01_T2w.nii
│       └── func
│           └── sub-3538_ses-2_run-01_task-rest_bold.nii
├── sub-3543
│   ├── ses-1
│   │   ├── anat
│   │   │   └── sub-3543_ses-1_run-01_T2w.nii
│   │   └── func
│   │       └── sub-3543_ses-1_run-01_task-rest_bold.nii
│   └── ses-2
│       ├── anat
│       │   └── sub-3543_ses-2_run-01_T2w.nii
│       └── func
│           └── sub-3543_ses-2_run-01_task-rest_bold.nii
├── sub-3545
│   ├── ses-1
│   │   ├── anat
│   │   │   └── sub-3545_ses-1_run-01_T2w.nii
│   │   └── func
│   │       └── sub-3545_ses-1_run-01_task-rest_bold.nii
│   └── ses-2
│       ├── anat
│       │   └── sub-3545_ses-2_run-01_T2w.nii
│       └── func
│           └── sub-3545_ses-2_run-01_task-rest_bold.nii
├── sub-3546
│   ├── ses-1
│   │   ├── anat
│   │   │   └── sub-3546_ses-1_run-01_T2w.nii
│   │   └── func
│   │       └── sub-3546_ses-1_run-01_task-rest_bold.nii
│   └── ses-2
│       ├── anat
│       │   └── sub-3546_ses-2_run-01_T2w.nii
│       └── func
│           └── sub-3546_ses-2_run-01_task-rest_bold.nii
├── sub-3547
│   ├── ses-1
│   │   ├── anat
│   │   │   └── sub-3547_ses-1_run-01_T2w.nii
│   │   └── func
│   │       └── sub-3547_ses-1_run-01_task-rest_bold.nii
│   └── ses-2
│       ├── anat
│       │   └── sub-3547_ses-2_run-01_T2w.nii
│       └── func
│           └── sub-3547_ses-2_run-01_task-rest_bold.nii
└── sub-3549
    ├── ses-1
    │   ├── anat
    │   │   └── sub-3549_ses-1_run-01_T2w.nii
    │   └── func
    │       └── sub-3549_ses-1_run-01_task-rest_bold.nii
    └── ses-2
        ├── anat
        │   └── sub-3549_ses-2_run-01_T2w.nii
        └── func
            └── sub-3549_ses-2_run-01_task-rest_bold.nii

135 directories, 78 files
Gab-D-G commented 3 years ago

Hi Christian, I believe the error might be in the specification of 'run-01' for the anatomical images, which are not supposed to have run specifications. Could you try running it again without the run spec?

ChristianNSchmitz commented 3 years ago

Sure, I'll let you know, when it's done

ChristianNSchmitz commented 3 years ago

The improved naming scheme solved this issue. However, a second error came up. You can find the log file attached:

rabies_preprocess.log terminal.txt

Gab-D-G commented 3 years ago

Hi Christian, the error is somehow triggered by your mask. I think it is most likely to be one of either two possible issues: 1-the masks you provided have some error, either they are not binary files, or were not properly overlapping with your template 2-the registration failed in the pipeline, so the masks are not overlapping with your files after registration. You could check the QC_report/ outputs to see if the registration worked out? You can see examples and guidelines about this step on the README. I hope this helps!

Best, Gabe

ChristianNSchmitz commented 3 years ago

Dear Gabe, thanks for all the support! I checked the masked files and they are binary. Furthermore, you can see the QC-reports of several animals and the registration seems to be alright. You can see one example here:

sub-3547_ses-2_run-01_task-rest_bold_EPI2Anat sub-3547_ses-2_T2w_Anat2Template

Gab-D-G commented 3 years ago

Hi Christian, if your masks are indeed binary and overlapping with the provided template I'm unsure what might be the cause... I saw that your masks are in the .nii file format, and I might have not corrected error cases with this format for the atlas files. Would you mind trying it again in a .nii.gz format? You can convert you files to .gz with the 'gzip' command.

ChristianNSchmitz commented 3 years ago

Dear Gabe, thanks for the support! I checked the masks again and, indeed, they wer not binary. As this problem was resolved and the preprocessing was completed, running the "confound_regression" part of the analysis gave me following error (same error as in the initial post above):

/mnt/d/PsiAlc/RabiesDir# docker run -it --rm -v /mnt/d/PsiAlc/Atlas/:/atlas -v /mnt/d/PsiAlc/RabiesDir/derivates/outputPreprocess/:/niiinputs:ro -v /mnt/d/PsiAlc/RabiesDir/derivates/outputConfoundRegression:/outputs gabdesgreg/rabies:latest confound_regression /niiinputs /outputs Traceback (most recent call last): File "/home/rabies/RABIES-0.2.0/exec.py", line 13, in execute_workflow() File "/home/rabies/RABIES-0.2.0/rabies/run_main.py", line 305, in execute_workflow workflow = confound_regression(opts, None, log) File "/home/rabies/RABIES-0.2.0/rabies/run_main.py", line 414, in confound_regression workflow = preprocess(preprocess_opts, opts, analysis_opts, log) File "/home/rabies/RABIES-0.2.0/rabies/run_main.py", line 385, in preprocess opts, cr_opts=cr_opts, analysis_opts=analysis_opts) File "/home/rabies/RABIES-0.2.0/rabies/main_wf.py", line 128, in init_main_wf layout, opts.bold_only) File "/home/rabies/RABIES-0.2.0/rabies/preprocess_pkg/utils.py", line 32, in prep_bids_iter "No anatomical file with the suffix 'T2w' or 'T1w' were found among the BIDS directory.") ValueError: No anatomical file with the suffix 'T2w' or 'T1w' were found among the BIDS directory.

You can find the log file here: rabies_confound_regression.log

And the tree of the original data: dir_tree.txt

Gab-D-G commented 3 years ago

Hi Christian, you are not the first to face this problem so it probably isn't clear enough in the README. When using RABIES in a container, you must provide consistent paths (from -v) between the different processing steps (preprocess, confound_regression, analysis). This is because subsequent steps after preprocess will try to read the folders that were used previously. In your case, I expect that the /niiinputs path was referring to your original dataset during the preprocess steps, and so the path names should remain consistent during the confound_regression step. If the outputPreprocess folder also had a given path name, you should keep it consistent. You can name the specify /mnt/d/PsiAlc/RabiesDir/derivates/outputConfoundRegression:/outputConfoundRegression for your outputs of the confound_regression step. Let me know if this isn't clear!

ChristianNSchmitz commented 3 years ago

Dear Gabe, thanks for all the support, the remark on the path-functionality of docker helped a lot!

I continued with the confound_regression analysis, however, it resulted in another error (I attached the log file as well as the terminal output of one animal):

terminal.txt rabies_confound_regression.log

Using this confound regression output in the analysis-step resultet in an empty analysis_datasink: rabies_analysis.log

grandjeanlab commented 3 years ago

steps

Hey @Gab-D-G , could you specify this in the README? e.g. give an example (same as you do for preprocess). I ran into same issue today, so it would help users.

Gab-D-G commented 3 years ago

@ChristianNSchmitz I am not sure if rabies_confound_regression.log is complete since I can't find any error in this log. For the analysis part, you don't get any outputs because you haven't selected any of the analysis option, and so none is run. You have to choose among FC_matrix, group_ICA, DR_ICA or providing seeds in seed_list for seed-based FC analysis. The analysis outputs are still limited, so I would recommend to make sure you know what type of analysis you want to achieve, and let me know if you have recommendations for improvements!

kuanjlee commented 3 years ago

Hi @Gab-D-G, it would be great if you could give us a Docker example script, that will run in its entirety (preprocessing, confound regression and analysis) for the example dataset that you supply, please. This will let us see both the command syntax as well as typical values for the input and output parameters/options that are at least guaranteed to work. Thanks!

Gab-D-G commented 3 years ago

Hi @kuanjlee, thank you for the suggestion! That's a good idea, I will add it soon to the documentation. In the meantime, maybe you could find this resource useful https://github.com/CoBrALab/documentation/wiki/Running-RABIES-on-niagara. There are some examples for running RABIES within a container.

Gab-D-G commented 3 years ago

@kuanjlee I have updated the README to have a clearer example for each processing steps using the test dataset, both with and without a container. I hope this will be helpful!

kuanjlee commented 3 years ago

Hi @Gab-D-G, thanks for your response. We tried the examples in the README on the test dataset using Docker as well as Singularity. Although we cut and pasted the relevant lines, there were still errors and the execution did not run to completion. Actually, there is a typo in your entry for confound_regression (extra “/” in front of “confound_regression”).

So we still don’t know if the problem lies with us or whether the instructions, dependencies and/or setup are incomplete. To improve reproducibility, could you include a makefile for the Docker/Singularity? Or let us have a clone of your own Docker/Singularity? Thanks!

Gab-D-G commented 3 years ago

Hi, thank you for the notice about the typo, I'll change it. Did you try downloading the container from docker hub following the instruction in the INSTALL.md https://github.com/CoBrALab/RABIES/blob/master/INSTALL.md? If not, this is how it is supposed to be downloaded. I would recommend trying singularity with singularity build rabies.sif docker://gabdesgreg/rabies:latest. If there are still errors, could you share the log file so that I can track the error? It is the .log files found in the output folder.

isacki commented 3 years ago

Hi @Gab-D-G, @kuanjlee and I did follow those steps. Preprocessing log does not mention an error, however it is missing QC_report/_Template2Commonspace.png. All other steps do not complete. Please see the attached script (I changed extension from .sh to .txt because can't upload .sh) and log files (for all 3 steps).

rabies_analysis.log rabies_confound_regression.log rabies_preprocess.log rabies_test_dataset_singularity.txt

Gab-D-G commented 3 years ago

Hi @isacki , it seems like the preprocessing step worked out. Do you find outputs in the QC_report folder and the datasink folders? For the confound_regression step, I realize the highpass filter is causing an error because the files in the test dataset are only 15 volumes I believe, which isn't long enough to apply a filter. I'll change that in the recommendations on the README, and you can try to run it again without --highpass 0.01 in the confound regression step.

isacki commented 3 years ago

Hi again @Gab-D-G , thanks for the tip as now confound_regression and analysis completed on your test dataset. We also tested it on a similar dataset of our own as we're looking at using it soon. We compared singularity and docker (same 0.2.1 version and parameters) and found there were differences in the Explained Variance plots - plots and relevant logs are attached. Would be good to know why there are differences and what is the best way to use it.

Test dataset: Plots differ between singularity and docker. Analysis log shows error for singularity only (line 168). Preprocessing logs have 2 registration errors (lines 7433 & 7457) in singularity, docker has 0, though starting registration metric is the same (line 912 under metricValue column).

testdataset_singularity_EVplot testdataset_singularity_preprocess.log testdataset_singularity_analysis.log testdataset_docker_EVplot testdataset_docker_preprocess.log testdataset_docker_analysis.log

Our dataset: Plots differ between singularity and docker (more subtly eg. intercept between x=50 & y=0.1). No errors in analysis log. Preprocessing logs have 2 registration errors (lines 7562 & 7593) in singularity to docker's 1 (line 7650); starting registration metric is different (line 918).

ourdataset_singularity_EVplot ourdataset_singularity_preprocess.log ourdataset_singularity_analysis.log ourdataset_docker_EVplot ourdataset_docker_preprocess.log ourdataset_docker_analysis.log

Gab-D-G commented 3 years ago

Hi @isacki , I'm not sure what's the source of the error here. Maybe some of the registrations failed with the singularity run. Did you check the QC_report to see if the processing was succesful? If not, that's most likely the source of the error.

gdevenyi commented 3 years ago

Closing this issue as it is a mix of a bunch of different requests and people.

Please open individual issues for any new problems and follow the issue template.