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nimh-dsst / dsst-defacing-pipeline

Defacing algorithm to improve and evaluate accuracy for large datasets.
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printing helpful summary info to stdout #13

Closed Arshitha closed 2 years ago

Arshitha commented 2 years ago

Here's an example of what the terminal output would look like:

(conda)[arshithab@helix dsst_defacing_wf]$ python generate_mappings.py -i /data/NIMH_scratch/defacing_comparisons/autism_subtypes/bids_20220527 -o examples/
==================================
VisualQC's visualqc_t1_mri command
==================================
Run the following command to QC primary scans:
 visualqc_t1_mri -u /gpfs/gsfs12/users/NIMH_scratch/defacing_comparisons/code/code_refactoring/dsst_defacing_wf/examples/visualqc_prep/t1_mri -i /gpfs/gsfs12/users/NIMH_scratch/defacing_comparisons/code/code_refactoring/dsst_defacing_wf/examples/visualqc_prep/id_list_t1.txt -m primary.nii.gz

====================
Dataset Summary
====================
Total number of sessions in the dataset: 263
Total number of sessions with at least one T1w scan: 250
Total number of sessions WITHOUT a T1w scan: 13
List of sessions without a T1w scan:
 ['sub-NDAREM381WD9/ses-01', 'sub-NDARINVKO353UAS/ses-01', 'sub-NDARBN729RG0/ses-01', 'sub-NDARINVHE728FXQ/ses-01', 'sub-NDARVG708MPB/ses-01', 'sub-NDARINVSE216ZSO/ses-02', 'sub-NDARZN020RY3/ses-04', 'sub-NDARWF021EZF/ses-01', 'sub-NDARBP915LD8/ses-01', 'sub-NDARWE296DLJ/ses-01', 'sub-NDARYN672VGP/ses-02', 'sub-NDARNB146TBN/ses-01', 'sub-NDARTX478BEP/ses-02']

Please find the mapping file JSON format and other helpful logs at /gpfs/gsfs12/users/NIMH_scratch/defacing_comparisons/code/code_refactoring/dsst_defacing_wf/examples.
ericearl commented 2 years ago

Resist the urge to put periods at the end of log statements with paths in them:

Please find the mapping file JSON format and other helpful logs at /gpfs/gsfs12/users/NIMH_scratch/defacing_comparisons/code/code_refactoring/dsst_defacing_wf/examples.