How to convert DICOM files in 'secondary' folder into 'NIFTI' using dcm2nii pipeline?

[Ruba]

Hi,

I am transferring PET scan files using 'compressed uploader' in XNAT. It creates secondary folder for some DICOM's. That's why, when I am using dcm2nii pipeline to convert the DICOM files, it shows session failure. How can I solve this problem?

Here is my log from PIPELINE_HOME:

Cause:  

org.nrg.pipeline.exception.PipelineEngineException: Unable to complete pipeline  Execution of dcm2nii -p N -d N -e N -f N -g N -n Y -r N -x N -o /data/xnat/build/FDOPA_STRATA1/20200418_154657/archive_trigger/20200418154657365/KCL141284_000022/NIFTI/501  /data/xnat/build/FDOPA_STRATA1/20200418_154657/archive_trigger/20200418154657365/KCL141284_000022/RAW/501 at Step[id= CONVERT:501] was unsuccesfull  Execution of dcm2nii -p N -d N -e N -f N -g N -n Y -r N -x N -o /data/xnat/build/FDOPA_STRATA1/20200418_154657/archive_trigger/20200418154657365/KCL141284_000022/NIFTI/501  /data/xnat/build/FDOPA_STRATA1/20200418_154657/archive_trigger/20200418154657365/KCL141284_000022/RAW/501 at Step[id= CONVERT:501] was unsuccesfull

at org.nrg.pipeline.manager.PipelineManager.launchPipeline(PipelineManager.java:226)

at org.nrg.pipeline.manager.PipelineManager.launchPipeline(PipelineManager.java:193)

at org.nrg.pipeline.client.XNATPipelineLauncher.launch(XNATPipelineLauncher.java:63)

at org.nrg.pipeline.client.XNATPipelineLauncher.run(XNATPipelineLauncher.java:298)

at org.nrg.pipeline.client.XNATPipelineLauncher.main(XNATPipelineLauncher.java:260)

]

Manage File Structure:

Thanks in advance.

- Ruba