Dear Fidel,
Thank you for your help so far.
I was trying to run the pipeline after compiling the docker image, and I followed the data structure as in: https://git.fmrib.ox.ac.uk/falmagro/UK_biobank_pipeline_v_1/-/blob/master/bb_data/ideal_config.json?ref_type=heads
Thus, for an exemplar subject 1, I gave just three MRI sequences, as below:
|-1
| |-dMRI
| | |-raw
| | | |-AP.bval
| | | |-AP.bvec
| | | |-AP.nii.gz
| |-T1
| | |-T1.nii.gz
| |-T2_FLAIR
| | |-T2_FLAIR.nii.gz
However, when trying to run the pipeline I get this:
================================================================================
2024-04-09 12:27:56,245 - bb_pipeline_queue - INFO - Starting the subject processing: Tue Apr 9 12:27:56 2024
2024-04-09 12:27:56,245 - bb_pipeline_queue - INFO - Subject received as input: 1
2024-04-09 12:27:56,245 - bb_pipeline_queue - INFO - Running file manager
2024-04-09 12:27:56,252 - bb_pipeline_queue - INFO - Performing action capitalize_and_clean on files with patterns *.*
2024-04-09 12:27:56,252 - bb_pipeline_queue - INFO - File names changed to upper case.
2024-04-09 12:27:56,252 - bb_pipeline_queue - INFO - Performing action move_to on files with patterns dicom
2024-04-09 12:27:56,252 - bb_pipeline_queue - INFO - Performing action move_to on files with patterns DICOM
2024-04-09 12:27:56,253 - bb_pipeline_queue - INFO - Performing action manage_struct on files with patterns T1*.nii.gz
2024-04-09 12:27:56,253 - bb_pipeline_queue - INFO - Performing action manage_struct on files with patterns MPRAGE*.nii.gz
2024-04-09 12:27:56,253 - bb_pipeline_queue - INFO - List of files received for struct processing: []
...
2024-04-09 12:27:56,261 - bb_pipeline_queue - ERROR - Subject cannot be run. There is no T1 or it has not the correct dimensions
2024-04-09 12:27:56,261 - bb_pipeline_queue - INFO - Main processing file finished at: Tue Apr 9 12:27:56 2024
=================================================================================
Note that T1 image has dimensions: 167 x 228 x 227.
I am not sure why is not loading/reading the T1.
Apologies in advance if I missed this information somewhere else.
Many Thanks
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