[ENH] Clarify meaning of raw vs derivative datasets #1537

CPernet · 2023-06-30T12:46:15Z

following the BIDS derivatives meeting

-closes #1523

follow the BIDS derivatives meeting

for more information, see https://pre-commit.ci

codecov · 2023-06-30T12:51:32Z

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src/derivatives/introduction.md

Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>

CPernet · 2023-06-30T13:58:59Z

I was preparing that in the guideline

A defaced T1w image can be derived from a BIDS datasets and is thus under derivatives

sub-01/anat/sub-01_T1w.nii.gz
derivatives/sub-01/anat/sub-01_desc-defaced_T1w.nii.gz

A defaced T1w image can be made during the curation process and is thus under raw

/sub-01/anat/sub-01_desc-defaced_T1w.nii.gz

yarikoptic · 2023-06-30T14:59:04Z

A defaced T1w image can be derived from a BIDS datasets and is thus under derivatives
sub-01/anat/sub-01_T1w.nii.gz
derivatives/sub-01/anat/sub-01_desc-defaced_T1w.nii.gz

when above would be used?

I would expect along your:

A defaced T1w image can be made during the curation process and is thus under raw

/sub-01/anat/sub-01_desc-defaced_T1w.nii.gz

to be

sub-01/anat/sub-01_desc-defaced_T1w.nii.gz
sourcedata/private/sub-01/anat/sub-01_T1w.nii.gz

or alike with sourcedata/private not being shared publicly, with _desc-defaced to have a clear indicator that it is defaced, with descriptions.tsv possibly describing briefly "how" (attn @robertoostenveld) and even .prov.jsonld somewhere (attn @cmaumet) giving details. ATM what we have is that all T1s in openneuro are defaced AFAIK and only 3 datasets have indicators about that with _rec- (_desc is indeed more appropriate if not done on scanner, then _proc -- ref #65 and #105) being abused for that purpose:

❯ cat T1ws.txt| grep def
ds004192/sub-01/ses-localizer1/anat/sub-01_ses-localizer1_acq-prescannormalized_rec-pydeface_T1w.nii.gz
ds004413/sub-20712/ses-12367/anat/sub-20712_ses-12367_rec-defaced_T1w.nii.gz
ds004450/sub-20712/ses-12367/anat/sub-20712_ses-12367_rec-defaced_T1w.nii.gz

here is a full list of sample T1w names

ds000001/sub-01/anat/sub-01_T1w.nii.gz
ds000002/sub-01/anat/sub-01_T1w.nii.gz
ds000003/sub-01/anat/sub-01_T1w.nii.gz
ds000005/sub-01/anat/sub-01_T1w.nii.gz
ds000006/sub-01/ses-retest/anat/sub-01_ses-retest_T1w.nii.gz
ds000007/sub-01/anat/sub-01_T1w.nii.gz
ds000008/sub-01/anat/sub-01_T1w.nii.gz
ds000009/sub-01/anat/sub-01_T1w.nii.gz
ds000011/sub-01/anat/sub-01_T1w.nii.gz
ds000017/sub-1/ses-timepoint1/anat/sub-1_ses-timepoint1_run-0_T1w.nii.gz
ds000030/sub-10159/anat/sub-10159_T1w.nii.gz
ds000031/sub-01/ses-015/anat/sub-01_ses-015_T1w.nii.gz
ds000051/sub-01/anat/sub-01_run-01_T1w.nii.gz
ds000052/sub-01/anat/sub-01_run-1_T1w.nii.gz
ds000053/sub-001/anat/sub-001_T1w.nii.gz
ds000101/sub-01/anat/sub-01_T1w.nii.gz
ds000102/sub-01/anat/sub-01_T1w.nii.gz
ds000105/sub-1/anat/sub-1_T1w.nii.gz
ds000107/sub-01/anat/sub-01_T1w.nii.gz
ds000108/sub-01/anat/sub-01_T1w.nii.gz
ds000109/sub-01/anat/sub-01_T1w.nii.gz
ds000110/sub-01/anat/sub-01_T1w.nii.gz
ds000113/sub-01/ses-forrestgump/anat/sub-01_ses-forrestgump_T1w.nii.gz
ds000114/sub-01/ses-retest/anat/sub-01_ses-retest_T1w.nii.gz
ds000115/sub-01/anat/sub-01_T1w.nii.gz
ds000116/sub-01/anat/sub-01_T1w.nii.gz
ds000117/sub-01/ses-mri/anat/sub-01_ses-mri_acq-mprage_T1w.nii.gz
ds000119/sub-01/anat/sub-01_T1w.nii.gz
ds000120/sub-01/anat/sub-01_T1w.nii.gz
ds000121/sub-01/anat/sub-01_T1w.nii.gz
ds000133/sub-01/ses-post/anat/sub-01_ses-post_T1w.nii.gz
ds000140/sub-01/anat/sub-01_T1w.nii.gz
ds000144/sub-01/anat/sub-01_T1w.nii.gz
ds000148/sub-01/anat/sub-01_acq-axial_run-01_T1w.nii.gz
ds000149/sub-01/anat/sub-01_T1w.nii.gz
ds000157/sub-01/anat/sub-01_T1w.nii.gz
ds000158/sub-001/anat/sub-001_T1w.nii.gz
ds000164/sub-001/anat/sub-001_T1w.nii.gz
ds000168/sub-01/anat/sub-01_T1w.nii.gz
ds000170/sub-1700/anat/sub-1700_T1w.nii.gz
ds000171/sub-control01/anat/sub-control01_T1w.nii.gz
ds000172/sub-control01/anat/sub-control01_T1w.nii.gz
ds000174/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz
ds000200/sub-2001/anat/sub-2001_T1w.nii.gz
ds000201/sub-9001/ses-1/anat/sub-9001_ses-1_T1w.nii.gz
ds000202/sub-1001/anat/sub-1001_T1w.nii.gz
ds000203/sub-01/anat/sub-01_T1w.nii.gz
ds000204/sub-01/ses-2011/anat/sub-01_ses-2011_T1w.nii.gz
ds000205/sub-01/anat/sub-01_T1w.nii.gz
ds000206/sub-THP0001/ses-THP0001CCF1/anat/sub-THP0001_ses-THP0001CCF1_run-01_T1w.nii.gz
ds000208/sub-01/anat/sub-01_T1w.nii.gz
ds000210/sub-01/anat/sub-01_T1w.nii.gz
ds000212/sub-03/anat/sub-03_T1w.nii.gz
ds000213/sub-01/anat/sub-01_T1w.nii.gz
ds000214/sub-EESS001/anat/sub-EESS001_T1w.nii.gz
ds000216/sub-01/anat/sub-01_T1w.nii.gz
ds000217/sub-Exp1s01/anat/sub-Exp1s01_T1w.nii.gz
ds000218/sub-01/anat/sub-01_T1w.nii.gz
ds000219/sub-01/anat/sub-01_T1w.nii.gz
ds000220/sub-control01/ses-1/anat/sub-control01_ses-1_T1w.nii.gz
ds000221/sub-010001/ses-02/anat/sub-010001_ses-02_acq-mp2rage_T1w.nii.gz
ds000222/sub-3107/anat/sub-3107_T1w.nii.gz
ds000223/sub-01/anat/sub-01_T1w.nii.gz
ds000224/sub-MSC01/ses-struct01/anat/sub-MSC01_ses-struct01_run-01_T1w.nii.gz
ds000228/sub-pixar001/anat/sub-pixar001_T1w.nii.gz
ds000229/sub-01/anat/sub-01_T1w.nii.gz
ds000231/sub-01/anat/sub-01_T1w.nii.gz
ds000232/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz
ds000233/sub-rid000001/anat/sub-rid000001_T1w.nii.gz
ds000234/sub-01/anat/sub-01_T1w.nii.gz
ds000235/sub-01/anat/sub-01_T1w.nii.gz
ds000236/sub-01/anat/sub-01_T1w.nii.gz
ds000237/sub-01/anat/sub-01_T1w.nii.gz
ds000238/sub-01/anat/sub-01_T1w.nii.gz
ds000239/sub-01/anat/sub-01_run-01_T1w.nii.gz
ds000240/sub-01/anat/sub-01_T1w.nii.gz
ds000241/sub-00/anat/sub-00_T1w.nii.gz
ds000243/sub-001/anat/sub-001_T1w.nii.gz
ds000244/sub-01/ses-00/anat/sub-01_ses-00_T1w.nii.gz
ds000245/sub-CTL01/anat/sub-CTL01_T1w.nii.gz
ds000246/sub-0001/anat/sub-0001_T1w.nii.gz
ds000247/sub-0002/ses-01/anat/sub-0002_ses-01_T1w.nii.gz
ds000248/sub-01/anat/sub-01_T1w.nii.gz
ds000249/sub-01/anat/sub-01_T1w.nii.gz
ds000253/sub-01/anat/sub-01_T1w.nii.gz
ds000254/BOLD for task-induced functional MRI/sub-01/anat/sub-01_T1w.nii.gz
ds000255/sub-01/ses-anat/anat/sub-01_ses-anat_T1w.nii.gz
ds000256/sub-CTS200/anat/sub-CTS200_T1w.nii.gz
ds000258/sub-04570/anat/sub-04570_T1w.nii.gz
ds001019/sub-01/anat/sub-01_T1w.nii.gz
ds001021/sub-A00008326/ses-DS2/anat/sub-A00008326_ses-DS2_T1w.nii.gz
ds001037/sub-CG/anat/sub-CG_T1w.nii.gz
ds001105/sub-001/anat/sub-001_T1w.nii.gz
ds001110/sub-01/anat/sub-01_T1w.nii.gz
ds001131/sub-01/anat/sub-01_T1w.nii.gz
ds001132/sub-01/anat/sub-01_T1w.nii.gz
ds001145/sub-01/anat/sub-01_T1w.nii.gz
ds001161/sub-22/anat/sub-22_run-01_T1w.nii.gz
ds001167/sub-19/anat/sub-19_run-01_T1w.nii.gz
ds001168/sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz
ds001178/sub-kate000/anat/sub-kate000_T1w.nii.gz
ds001218/sub-002/anat/sub-002_T1w.nii.gz
ds001226/sub-CON01/ses-preop/anat/sub-CON01_ses-preop_T1w.nii.gz
ds001228/sub-02/anat/sub-02_T1w.nii.gz
ds001229/sub-01/anat/sub-01_T1w.nii.gz
ds001232/sub-01/anat/sub-01_T1w.nii.gz
ds001233/sub-01/ses-pre/anat/sub-01_ses-pre_T1w.nii.gz
ds001241/sub-01/anat/sub-01_T1w.nii.gz
ds001242/sub-01/anat/.bidsignore_sub-01_melanin_T1w.nii.gz
ds001246/sub-01/ses-anatomy/anat/sub-01_ses-anatomy_T1w.nii.gz
ds001247/sub-1/anat/sub-1_T1w.nii.gz
ds001297/sub-01/anat/sub-01_T1w.nii.gz
ds001299/sub-02003/ses-01/anat/sub-02003_ses-01_run-01_T1w.nii.gz
ds001302/sub-02/anat/sub-02_T1w.nii.gz
ds001306/sub-02/anat/sub-02_T1w.nii.gz
ds001338/sub-tb2994/anat/sub-tb2994_T1w.nii.gz
ds001344/sub-001/ses-scan1/anat/sub-001_ses-scan1_T1w.nii.gz
ds001345/sub-01/anat/sub-01_T1w.nii.gz
ds001353/sub-8107/anat/sub-8107_run-01_T1w.nii.gz
ds001354/sub-cntrl01/anat/sub-cntrl01_T1w.nii.gz
ds001357/sub-001/anat/sub-001_T1w.nii.gz
ds001365/sub-01/anat/sub-01_T1w.nii.gz
ds001371/sub-M80301092/anat/sub-M80301092_T1w.nii.gz
ds001378/sub-SCA201/ses-01/anat/sub-SCA201_ses-01_T1w.nii.gz
ds001379/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz
ds001386/sub-01/anat/sub-01_T1w.nii.gz
ds001399/sub-MOCCAG001/ses-01/anat/sub-MOCCAG001_ses-01_T1w.nii.gz
ds001408/sub-NF01/ses-1preEEG/anat/sub-NF01_ses-1preEEG_T1w.nii.gz
ds001415/sub-01/anat/sub-01_T1w.nii.gz
ds001417/sub-study002/ses-after/anat/sub-study002_ses-after_T1w.nii.gz
ds001419/sub-01/anat/sub-01_T1w.nii.gz
ds001430/sub-01/anat/sub-01_T1w.nii.gz
ds001439/sub-04/anat/sub-04_T1w.nii.gz
ds001454/sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz
ds001482/sub-401/anat/sub-401_T1w.nii.gz
ds001486/sub-001/ses-T1/anat/sub-001_ses-T1_T1w.nii.gz
ds001491/sub-01/anat/sub-01_T1w.nii.gz
ds001497/sub-01/anat/sub-01_T1w.nii.gz
ds001499/sub-CSI1/ses-16/anat/sub-CSI1_ses-16_run-01_T1w.nii.gz
ds001506/sub-01/ses-anatomy/anat/sub-01_ses-anatomy_T1w.nii.gz
ds001510/sub-01/anat/sub-01_T1w.nii.gz
ds001511/sub-sid000001/anat/sub-sid000001_T1w.nii.gz
ds001517/sub-01/anat/sub-01_T1w.nii.gz
ds001521/sub-01/anat/sub-01_T1w.nii.gz
ds001534/sub-01/anat/sub-01_T1w.nii.gz
ds001545/sub-01/anat/sub-01_T1w.nii.gz
ds001551/sub-0055/anat/sub-0055_T1w.nii.gz
ds001553/sub-001/ses-01/anat/sub-001_ses-01_run-001_T1w.nii.gz
ds001554/sub-01/anat/sub-01_T1w.nii.gz
ds001555/sub-001/ses-01/anat/sub-001_ses-01_acq-MPRAGE_run-001_T1w.nii.gz
ds001566/sub-01/anat/sub-01_T1w.nii.gz
ds001576/sub-01/anat/sub-01_T1w.nii.gz
ds001583/sub-SS30/anat/sub-SS30_T1w.nii.gz
ds001590/sub-01/anat/sub-01_T1w.nii.gz
ds001595/sub-1/anat/sub-1_T1w.nii.gz
ds001597/sub-01/ses-pre/anat/sub-01_ses-pre_T1w.nii.gz
ds001600/sub-1/anat/sub-1_T1w.nii.gz
ds001607/sub-01/anat/sub-01_T1w.nii.gz
ds001608/sub-01/anat/sub-01_T1w.nii.gz
ds001612/sub-01/anat/sub-01_T1w.nii.gz
ds001614/sub-01/anat/sub-01_T1w.nii.gz
ds001619/sub-M80303814/anat/sub-M80303814_ce-echo1_T1w.nii.gz
ds001621/sub-01/anat/sub-01_T1w.nii.gz
ds001634/sub-01/anat/sub-01_T1w.nii.gz
ds001635/sub-01/anat/sub-01_T1w.nii.gz
ds001715/sub-01/anat/sub-01_T1w.nii.gz
ds001722/sub-01/anat/sub-01_T1w.nii.gz
ds001728/sub-01/anat/sub-01_T1w.nii.gz
ds001734/sub-001/anat/sub-001_T1w.nii.gz
ds001740/sub-01/anat/sub-01_T1w.nii.gz
ds001743/sub-01/anat/sub-01_T1w.nii.gz
ds001745/sub-01/anat/sub-01_T1w.nii.gz
ds001747/sub-2975/anat/sub-2975_run-01_T1w.nii.gz
ds001748/sub-adult01/anat/sub-adult01_T1w.nii.gz
ds001751/sub-01/anat/sub-01_T1w.nii.gz
ds001761/sub-01/ses-01/anat/sub-01_ses-01_acq-01_T1w.nii.gz
ds001762/sub-01/anat/sub-01_T1w.nii.gz
ds001771/sub-03/anat/sub-03_T1w.nii.gz
ds001775/sub-01/anat/sub-01_T1w.nii.gz
ds001780/sub-01/anat/sub-01_T1w.nii.gz
ds001784/sub-01/anat/sub-01_T1w.nii.gz
ds001796/bidsignore/sub-201/anat/sub-201_T1w.nii.gz
ds001814/sub-hc001/anat/sub-hc001_T1w.nii.gz
ds001818/sub-001/ses-01/anat/sub-001_ses-01_T1w.nii.gz
ds001832/sub-01/ses-0/anat/sub-01_ses-0_T1w.nii.gz
ds001838/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz
ds001839/sub-5879027/anat/sub-5879027_T1w.nii.gz
ds001840/sub-04/anat/sub-04_T1w.nii.gz
ds001847/sub-01/anat/sub-01_T1w.nii.gz
ds001848/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz
ds001868/sub-ecog01/ses-postimp/anat/sub-ecog01_ses-postimp_T1w.nii.gz
ds001875/sub-01/anat/sub-01_T1w.nii.gz
ds001882/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz
ds001883/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz
ds001894/sub-001/ses-T1/anat/sub-001_ses-T1_T1w.nii.gz
ds001907/sub-RC4101/ses-1/anat/sub-RC4101_ses-1_T1w.nii.gz
ds001912/sub-01/ses-01/anat/sub-01_ses-01_run-01_T1w.nii.gz
ds001919/sub-amu01/anat/sub-amu01_T1w.nii.gz
ds001921/sub-01/anat/sub-01_T1w.nii.gz
ds001923/sub-01/anat/sub-01_T1w.nii.gz
ds001926/sub-01/ses-day1/anat/sub-01_ses-day1_T1w.nii.gz
ds001927/sub-s001/ses-ctr/anat/sub-s001_ses-ctr_T1w.nii.gz
ds001928/sub-01/anat/sub-01_T1w.nii.gz
ds001942/sub-S01/ses-SES01/anat/sub-S01_ses-SES01_acq-ShortInv_run-01_T1w.nii.gz
ds001946/sub-01/anat/sub-01_T1w.nii.gz
ds001966/sub-01/anat/sub-01_T1w.nii.gz
ds001972/sub-0008/ses-01/anat/sub-0008_ses-01_run-01_T1w.nii.gz
ds001978/sub-0045/ses-01/anat/sub-0045_ses-01_run-01_T1w.nii.gz
ds002006/sub-02/anat/sub-02_T1w.nii.gz
ds002011/sub-01/anat/sub-01_T1w.nii.gz
ds002014/sub-01/anat/sub-01_T1w.nii.gz
ds002016/sub-ICBM2009asym/anat/sub-ICBM2009asym_rez-500um_T1w.nii.gz
ds002033/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz
ds002041/sub-2001/anat/sub-2001_T1w.nii.gz
ds002076/sub-01/anat/sub-01_T1w.nii.gz
ds002080/sub-CON02/ses-postop/anat/sub-CON02_ses-postop_T1w.nii.gz
ds002105/sub-02/ses-a1/anat/sub-02_ses-a1_T1w.nii.gz
ds002116/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz
ds002149/sub-001/anat/sub-001_run-01_T1w.nii.gz
ds002155/sub-05/anat/sub-05_T1w.nii.gz
ds002156/sub-23638/ses-04/anat/sub-23638_ses-04_acq-mprage_rec-ORIG_run-1_T1w.nii.gz
ds002158/sub-02/ses-001/anat/sub-02_ses-001_run-001_T1w.nii.gz
ds002165/sub-01/ses-01/anat/sub-01_ses-01_acq-FullExample_run-01_T1w.nii.gz
ds002168/sub-1425/anat/sub-1425_T1w.nii.gz
ds002169/sub-01/anat/sub-01_T1w.nii.gz
ds002185/sub-01/anat/sub-01_T1w.nii.gz
ds002207/sub-01/anat/sub-01_T1w.nii.gz
ds002236/sub-01/anat/sub-01_T1w.nii.gz
ds002237/sub-01/anat/sub-01_T1w.nii.gz
ds002241/sub-01/anat/sub-01_T1w.nii.gz
ds002242/sub-1295/anat/sub-1295_T1w.nii.gz
ds002250/sub-01/anat/sub-01_run-01_T1w.nii.gz
ds002270/sub-01/anat/sub-01_T1w.nii.gz
ds002278/sub-PILOT/ses-01/anat/sub-PILOT_ses-01_run-01_T1w.nii.gz
ds002293/sub-001/anat/sub-001_T1w.nii.gz
ds002294/sub-002/anat/sub-002_T1w.nii.gz
ds002295/sub-02/ses-anat/anat/sub-02_ses-anat_acq-memp2rage_T1w.nii.gz
ds002306/sub-01/anat/sub-01_T1w.nii.gz
ds002307/sub-Ey112/ses-1/anat/sub-Ey112_ses-1_acq-RARE_T1w.nii.gz
ds002311/sub-01/anat/sub-01_T1w.nii.gz
ds002316/sub-119/anat/sub-119_T1w.nii.gz
ds002320/sub-01/anat/sub-01_T1w.nii.gz
ds002322/sub-18/anat/sub-18_T1w.nii.gz
ds002328/sub-01/anat/sub-01_T1w.nii.gz
ds002330/sub-01/anat/sub-01_T1w.nii.gz
ds002336/sub-xp101/anat/sub-xp101_T1w.nii.gz
ds002338/sub-xp201/anat/sub-xp201_T1w.nii.gz
ds002345/sub-001/anat/sub-001_T1w.nii.gz
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ds004173/sub-000103/anat/sub-000103_acq-headmotion1_T1w.nii.gz
ds004187/sub-01/anat/sub-01_T1w.nii.gz
ds004192/sub-01/ses-localizer1/anat/sub-01_ses-localizer1_acq-prescannormalized_rec-pydeface_T1w.nii.gz
ds004194/sub-p01/ses-umcu3t01/anat/sub-p01_ses-umcu3t01_run-01_T1w.nii.gz
ds004196/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz
ds004197/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz
ds004199/sub-00001/anat/sub-00001_acq-iso08_T1w.nii.gz
ds004215/sourcedata/sub-ON05258/ses-01/anat/sub-ON05258_ses-01_acq-MPRAGE_rec-SCIC_T1w.nii.gz
ds004217/sub-002/anat/sub-002_T1w.nii.gz
ds004219/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz
ds004226/sub-001/anat/sub-001_T1w.nii.gz
ds004228/sub-01/ses-01/anat/sub-01_ses-01_run-01_T1w.nii.gz
ds004230/sub-PS19/ses-baselinebrain/anat/sub-PS19_ses-baselinebrain_T1w.nii.gz
ds004241/sub-C001/anat/sub-C001_acq-MP2RAGE_run-01_T1w.nii.gz
ds004253/sub-103111/anat/sub-103111_acq-MP2RAGE_T1w.nii.gz
ds004259/sub-1/anat/sub-1_acq-11_T1w.nii.gz
ds004265/sub-01/anat/sub-01_T1w.nii.gz
ds004271/sub-001/ses-03/anat/sub-001_ses-03_acq-ADNI_run-01_T1w.nii.gz
ds004283/sub-01/ses-02/anat/sub-01_ses-02_T1w.nii.gz
ds004285/sub-01/anat/sub-01_T1w.nii.gz
ds004286/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz
ds004288/sub-0010/anat/sub-0010_T1w.nii.gz
ds004298/sub-087/anat/sub-087_run-01_T1w.nii.gz
ds004299/sub-103/ses-1/anat/sub-103_ses-1_T1w.nii.gz
ds004301/sub-01/anat/sub-01_T1w.nii.gz
ds004302/sub-01/anat/sub-01_T1w.nii.gz
ds004312/sub-060/ses-01/anat/sub-060_ses-01_T1w.nii.gz
ds004331/sub-01/anat/sub-01_T1w.nii.gz
ds004339/sub-001/anat/sub-001_T1w.nii.gz
ds004346/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz
ds004349/sub-1/anat/sub-1_T1w.nii.gz
ds004360/sub-101/ses-2/anat/sub-101_ses-2_T1w.nii.gz
ds004392/sub-0202/ses-01/anat/sub-0202_ses-01_T1w.nii.gz
ds004393/sub-01/anat/sub-01_T1w.nii.gz
ds004400/sub-01/anat/sub-01_T1w.nii.gz
ds004401/sub-dummy/anat/sub-dummy_T1w.nii.gz
ds004406/sub-02/ses-01/anat/sub-02_ses-01_T1w.nii.gz
ds004413/sub-20712/ses-12367/anat/sub-20712_ses-12367_rec-defaced_T1w.nii.gz
ds004440/sub-ACM07/ses-stanfordCNI/anat/sub-ACM07_ses-stanfordCNI_run-01_T1w.nii.gz
ds004443/sub-0201/ses-01/anat/sub-0201_ses-01_T1w.nii.gz
ds004450/sub-20712/ses-12367/anat/sub-20712_ses-12367_rec-defaced_T1w.nii.gz
ds004455/sub-00001/anat/sub-00001_T1w.nii.gz
ds004456/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz
ds004466/sub-CISC13877/anat/sub-CISC13877_T1w.nii.gz
ds004470/sub-C001/anat/sub-C001_acq-MP2RAGE_run-01_T1w.nii.gz
ds004471/sub-087/anat/sub-087_run-01_T1w.nii.gz
ds004473/sub-1/anat/sub-1_T1w.nii.gz
ds004478/sub-01/anat/sub-01_T1w.nii.gz
ds004484/sub-01/anat/sub-01_T1w.nii.gz
ds004488/sub-01/ses-action01/anat/sub-01_ses-action01_run-01_T1w.nii.gz
ds004489/sub-1014/ses-1/anat/sub-1014_ses-1_T1w.nii.gz
ds004493/sub-01/anat/sub-01_T1w.nii.gz
ds004496/sub-01/ses-anat/anat/sub-01_ses-anat_run-01_T1w.nii.gz
ds004498/sub-CIMT001/ses-38659/anat/sub-CIMT001_ses-38659_run-01_T1w.nii.gz
ds004509/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz
ds004513/sub-s003/ses-closed/anat/sub-s003_ses-closed_T1w.nii.gz
ds004544/sub-4793/anat/sub-4793_T1w.nii.gz
ds004552/sub-01/ses-01/anat/sub-01_ses-01_run-1_T1w.nii.gz
ds004553/sub-003/anat/sub-003_T1w.nii.gz
ds004556/sub-02/anat/sub-02_acq-mprage_run-1_T1w.nii.gz
ds004557/sub-01/ses-1/anat/sub-01_ses-1_acq-mprage_run-1_T1w.nii.gz
ds004560/sub-POBHC0001/ses-17473A/anat/sub-POBHC0001_ses-17473A_acq-TI1100TR1840_run-1_T1w.nii.gz
ds004564/sub-17017/anat/sub-17017_T1w.nii.gz
ds004590/sub-01/ses-001/anat/sub-01_ses-001_T1w.nii.gz
ds004592/sub-001/ses-01/anat/sub-001_ses-01_T1w.nii.gz
ds004597/sub-01/anat/sub-01_T1w.nii.gz
ds004620/sub-M13B/ses-20230406/anat/sub-M13B_ses-20230406_T1w.nii.gz

CPernet · 2023-07-03T06:03:55Z

I'd maybe rephrase case 1 and switch cases around- as you are right this is an unlikely scenario

A defaced T1w image would typically be made during the curation process and is thus under raw

/sub-01/anat/sub-01_desc-defaced_T1w.nii.gz
sourcedata/private/sub-01/anat/sub-01_T1w.nii.gz

A defaced T1w image could also, in theory, be derived from a BIDS dataset and would thus be under derivatives

sub-01/anat/sub-01_T1w.nii.gz
derivatives/sub-01/anat/sub-01_desc-defaced_T1w.nii.gz

yarikoptic · 2023-07-05T18:37:46Z

FWIW -- the above sounds good/correct to me as what is allowable etc. (minor note: inconsistent leading /)

add examples

for more information, see https://pre-commit.ci

CPernet · 2023-07-05T18:57:25Z

cool - added these to file now ; just need another review

src/derivatives/introduction.md

CPernet · 2023-07-10T12:39:27Z

sure, looks better (and fix desc-)

Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>

src/derivatives/introduction.md

For consistency

define raw and derivatives.md

7ca422f

follow the BIDS derivatives meeting

CPernet added the derivatives label Jun 30, 2023

CPernet requested review from yarikoptic and effigies June 30, 2023 12:46

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Update src/derivatives/introduction.md

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Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>

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Update introduction.md

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add examples

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Update src/derivatives/introduction.md

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Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>

Update src/derivatives/introduction.md

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Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>

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FIX: Update code fences

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effigies changed the title ~~define raw and derivatives.md~~ [ENH] Clarify meaning of raw vs derivative datasets Jul 11, 2023

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FIX: folders -> directory

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sappelhoff requested review from yarikoptic, ericearl and Remi-Gau July 24, 2023 14:48

CPernet merged commit 39263f1 into master Jul 24, 2023
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[DOC] Auto-generate changelog entry for PR #1537

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BEP021: Electrophysiological Derivatives #1680

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[ENH] Clarify meaning of raw vs derivative datasets #1537

[ENH] Clarify meaning of raw vs derivative datasets #1537

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CPernet commented Jul 10, 2023

[ENH] Clarify meaning of raw vs derivative datasets #1537

[ENH] Clarify meaning of raw vs derivative datasets #1537

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