Better match workflows #20
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sessions/runs into file names. Presently output of this pipeline is
as follows:
$ tree derivatives/
derivatives/
└── petdeface
├── dataset_description.json
├── sub-PS50
│ └── anat
│ ├── sub-PS50_T1w_defaced.nii
│ └── sub-PS50_T1w_facemask.nii
├── sub-PS50_ses-baseline
│ └── pet
│ ├── registration.lta
│ └── sub-PS50_ses-baseline_pet_defaced.nii.gz
└── sub-PS50_ses-blocked
└── pet
├── registration.lta
└── sub-PS50_ses-blocked_pet_defaced.nii.gz
7 directories, 7 files
At the least we need to label the regstration files better so
we don't get collisions if we flatten this out by subject.
|
Current status of Friday the 🦇 13th 🦇 $ for FOLDER in COX*; do tree $FOLDER/derivatives/petdeface; done
COX-1_analysis_faced_anat_in_each_session_folder/derivatives/petdeface
├── dataset_description.json
├── sub-PS50_ses-baseline
│ ├── anat
│ │ ├── sub-PS50_ses-baseline_T1w_defaced.nii
│ │ └── sub-PS50_ses-baseline_T1w_facemask.nii
│ └── pet
│ ├── registration.lta
│ └── sub-PS50_ses-baseline_pet_defaced.nii.gz
└── sub-PS50_ses-blocked
├── anat
│ ├── sub-PS50_ses-blocked_T1w_defaced.nii
│ └── sub-PS50_ses-blocked_T1w_facemask.nii
└── pet
├── registration.lta
└── sub-PS50_ses-blocked_pet_defaced.nii.gz
6 directories, 9 files
COX-1_analysis_faced_anat_in_first_session_folder/derivatives/petdeface
├── dataset_description.json
├── sub-PS50_ses-baseline
│ ├── anat
│ │ ├── sub-PS50_ses-baseline_T1w_defaced.nii
│ │ └── sub-PS50_ses-baseline_T1w_facemask.nii
│ └── pet
│ ├── registration.lta
│ └── sub-PS50_ses-baseline_pet_defaced.nii.gz
└── sub-PS50_ses-blocked
└── pet
├── registration.lta
└── sub-PS50_ses-blocked_pet_defaced.nii.gz
5 directories, 7 files
COX-1_analysis_faced_inherit_anat/derivatives/petdeface
├── dataset_description.json
├── sub-PS50
│ └── anat
│ ├── sub-PS50_T1w_defaced.nii
│ └── sub-PS50_T1w_facemask.nii
├── sub-PS50_ses-baseline
│ └── pet
│ ├── registration.lta
│ └── sub-PS50_ses-baseline_pet_defaced.nii.gz
└── sub-PS50_ses-blocked
└── pet
├── registration.lta
└── sub-PS50_ses-blocked_pet_defaced.nii.gz
6 directories, 7 files |
|
Pretty close to outputting proper bids directly to the derivatives directory, should be much easier now that I'm able to keep track of what workflow files belong to what inputs. |
|
@bilgelm tagging |
bilgelm
approved these changes
Oct 22, 2023
| "No T1w images found for participant {}. " | ||
| "All workflows require T1w images.".format(subject_id) | ||
| ) | ||
| data = collect_anat_and_pet(bids_data) |
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Looks like the pet-mri matching is now being done by this petutils function. Cool!
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This fixes many of this issues that pop up when petdeface encounters different BIDS layouts, mostly:
Will convert from draft when it's complete.