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McIntosh-Lab / tvb-ukbb

TVB-UKBB Pipeline: TheVirtualBrain implementation of the UK Biobank pipeline
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bianca_class_data not found and not available on UK Biobank website #20

Closed noahfl closed 4 years ago

noahfl commented 4 years ago

BIANCA needs files bianca_class_data and bianca_class_data_labels to be in bb_data in order to run.

bb_data has files bianca_class_data.txt and bianca_class_data_labels.txt and each contain links to the following respective sites:

https://www.win.ox.ac.uk//datasets/ukbiobank/bianca_class_data

https://www.win.ox.ac.uk//datasets/ukbiobank/bianca_class_data_labels

but both of these links are dead. Looking around for the new ones.

Traceback below:

+ echo /liberatrix/mcintosh_lab/nfrazier-logue/sub-002S0413/T1/T1_unbiased_brain.nii.gz /liberatrix/mcintosh_lab/nfrazier-logue/sub-002S0413/T2_FLAIR/T2_FLAIR_unbiased.nii.gz /liberatrix/mcintosh_lab/nfrazier-logue/sub-002S0413/T1/transforms/T1_to_MNI_linear.mat                                                                                                                                                                                            
+ /opt/HCPpipelines-4.1.3/fsl/bin/bianca --singlefile=sub-002S0413/T2_FLAIR/lesions/conf_file.txt --querysubjectnum=1 --brainmaskfeaturenum=1 --loadclassifierdata=/liberatrix/mcintosh_lab/ukbb/UK_biobank_pipeline_v_1/bb_data/bianca_class_data --matfeaturenum=3 --featuresubset=1,2 -o sub-002S0413/T2_FLAIR/lesions/bianca_mask                                                                                                                             
Traceback (most recent call last):                                                                                                                                                                                               
  File "/opt/HCPpipelines-4.1.3/fsl/bin/bianca", line 1033, in <module>                                                                                                                                                          
    p_main()                                                                                                                                                                                                                     
  File "/opt/HCPpipelines-4.1.3/fsl/bin/bianca", line 979, in p_main                                                                                                                                                             
    training_dat = pickle.load(open(GlobalOpts.load_classifier, 'rb'))                                                                                                                                                           
FileNotFoundError: [Errno 2] No such file or directory: '/liberatrix/mcintosh_lab/ukbb/UK_biobank_pipeline_v_1/bb_data/bianca_class_data'
noahfl commented 4 years ago

Files found at https://www.fmrib.ox.ac.uk/ukbiobank/fbp/. I downloaded them and added them to the directory; will link to pull request once I push it up.

noahfl commented 4 years ago

confirmed that this branch fixes BIANCA issue. structural pipeline now runs to completion without any errors.