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datalad / datalad-ukbiobank

Resources for working with UKBiobank as a DataLad dataset
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Missing json files for BIDS layout #81

Closed ltetrel closed 2 years ago

ltetrel commented 2 years ago

Hi,

I am using datalad-ukbiobank with pre-downloaded data, to convert the downloaded archive into a BIDS compliant dataset. However, I don't see any json files associated with the niftii images, is it expected ?

I run the following:

datalad create ${output_dir}/sub-${participant_id}
cd ${output_dir}/sub-${participant_id}
datalad ukb-init --bids --force ${participant_id} 20227_2_0 20252_2_0
datalad ukb-update --merge --force --keyfile ${keyfile_path}

And here the content of the BIDS dataset:

.
└── sub-1159104
    └── ses-2
        ├── anat
        │   └── sub-1159104_ses-2_T1w.nii.gz -> ../../.git/annex/objects/ww/xf/MD5E-s13185752--68ed198d992da40e39d220e7358e97bc.nii.gz/MD5E-s13185752--68ed198d992da40e39d220e7358e97bc.nii.gz
        ├── func
        │   ├── sub-1159104_ses-2_task-hariri_sbref.nii.gz -> ../../.git/annex/objects/Q4/9M/MD5E-s850576--76d9f31599639ba9cc7c12c6d40b52b9.nii.gz/MD5E-s850576--76d9f31599639ba9cc7c12c6d40b52b9.nii.gz
        │   └── sub-1159104_ses-2_task-rest_bold.nii.gz -> ../../.git/annex/objects/2K/xM/MD5E-s384519774--4f8059fea8a822f4945c11ef3ec0b022.nii.gz/MD5E-s384519774--4f8059fea8a822f4945c11ef3ec0b022.nii.gz
        └── non-bids
            ├── fMRI
            │   ├── rfMRI_100.dr
            │   │   └── dr_stage1.txt -> ../../../../.git/annex/objects/jz/6M/MD5E-s658825--01c0101a0ab68f5185abd1430855a700.txt/MD5E-s658825--01c0101a0ab68f5185abd1430855a700.txt
            │   ├── rfMRI_25.dr
            │   │   └── dr_stage1.txt -> ../../../../.git/annex/objects/F6/8W/MD5E-s160316--18925e533b1dc16b423d2569dd2a82f4.txt/MD5E-s160316--18925e533b1dc16b423d2569dd2a82f4.txt
            │   └── rfMRI.ica
            │       ├── absbrainthresh.txt -> ../../../../.git/annex/objects/xx/KP/MD5E-s7--af9a779a7d48a1a5f1cddf0bde3b238b.txt/MD5E-s7--af9a779a7d48a1a5f1cddf0bde3b238b.txt
            │       ├── design.fsf -> ../../../../.git/annex/objects/10/Xv/MD5E-s7844--b5f65beee695ef9a19b61a1db4f2eb22.fsf/MD5E-s7844--b5f65beee695ef9a19b61a1db4f2eb22.fsf
            │       ├── example_func.nii.gz -> ../../../../.git/annex/objects/K5/21/MD5E-s1471475--a95c366c2d28d13f2db90e2549818fc5.nii.gz/MD5E-s1471475--a95c366c2d28d13f2db90e2549818fc5.nii.gz
            │       ├── filtered_func_data_clean.nii.gz -> ../../../../.git/annex/objects/21/gW/MD5E-s271074906--a87d26296349e9dd8519741128f647a5.nii.gz/MD5E-s271074906--a87d26296349e9dd8519741128f647a5.nii.gz
            │       ├── filtered_func_data.ica
            │       │   ├── log.txt -> ../../../../../.git/annex/objects/p9/vq/MD5E-s44357--e0dcd5a19bc83320527ba7fc092166cc.txt/MD5E-s44357--e0dcd5a19bc83320527ba7fc092166cc.txt
            │       │   ├── mask.nii.gz -> ../../../../../.git/annex/objects/2J/7q/MD5E-s14857--eae5ac170963e772c748159687c3e2ad.nii.gz/MD5E-s14857--eae5ac170963e772c748159687c3e2ad.nii.gz
            │       │   ├── mean.nii.gz -> ../../../../../.git/annex/objects/p9/Kq/MD5E-s553118--6bf2e937ff9fada684b7a049e7d6029a.nii.gz/MD5E-s553118--6bf2e937ff9fada684b7a049e7d6029a.nii.gz
            │       │   ├── melodic_FTmix -> ../../../../../.git/annex/objects/f6/00/MD5E-s597412--12bdf986ec9521c91de76679d3ba55b1/MD5E-s597412--12bdf986ec9521c91de76679d3ba55b1
            │       │   ├── melodic_IC.nii.gz -> ../../../../../.git/annex/objects/q4/V1/MD5E-s109324412--55c691985e03d1284cfa6c6e85433ddf.nii.gz/MD5E-s109324412--55c691985e03d1284cfa6c6e85433ddf.nii.gz
            │       │   ├── melodic_ICstats -> ../../../../../.git/annex/objects/9G/PP/MD5E-s8043--cd962f3faa199f8fc29674db33c0d02a/MD5E-s8043--cd962f3faa199f8fc29674db33c0d02a
            │       │   ├── melodic_mix -> ../../../../../.git/annex/objects/2f/MK/MD5E-s1313864--fbc89bb9c47b31d57136dbee33bb0d96/MD5E-s1313864--fbc89bb9c47b31d57136dbee33bb0d96
            │       │   ├── melodic_PPCA -> ../../../../../.git/annex/objects/PG/G4/MD5E-s44662--6b015d3d7b229fec1d748ceb7e9d4fff/MD5E-s44662--6b015d3d7b229fec1d748ceb7e9d4fff
            │       │   └── melodic_Tmodes -> ../../../../../.git/annex/objects/2f/MK/MD5E-s1313864--fbc89bb9c47b31d57136dbee33bb0d96/MD5E-s1313864--fbc89bb9c47b31d57136dbee33bb0d96
            │       ├── fix4melview_UKBiobank_thr20.txt -> ../../../../.git/annex/objects/0Q/Gq/MD5E-s6257--2ec348c000604ebd1f074394fec4f753.txt/MD5E-s6257--2ec348c000604ebd1f074394fec4f753.txt
            │       ├── mask.nii.gz -> ../../../../.git/annex/objects/P9/1x/MD5E-s14846--785df6b1b9d0a7217c034d3bf3aa5edd.nii.gz/MD5E-s14846--785df6b1b9d0a7217c034d3bf3aa5edd.nii.gz
            │       ├── mc
            │       │   ├── disp.png -> ../../../../../.git/annex/objects/Xf/QM/MD5E-s5148--edc8e9f7bf6b5dcc64d2460feb1bd2b0.png/MD5E-s5148--edc8e9f7bf6b5dcc64d2460feb1bd2b0.png
            │       │   ├── prefiltered_func_data_mcf_abs_mean.rms -> ../../../../../.git/annex/objects/V5/M8/MD5E-s8--e45161698eb23bea634aaf1d7e98e5fa.rms/MD5E-s8--e45161698eb23bea634aaf1d7e98e5fa.rms
            │       │   ├── prefiltered_func_data_mcf_abs.rms -> ../../../../../.git/annex/objects/2W/w1/MD5E-s3912--28d92c3404c03f46f65ff4ca7d5cc8f7.rms/MD5E-s3912--28d92c3404c03f46f65ff4ca7d5cc8f7.rms
            │       │   ├── prefiltered_func_data_mcf.cat -> ../../../../../.git/annex/objects/GM/K6/MD5E-s74489--dcd356fb01ba626dea5974fbbc062557.cat/MD5E-s74489--dcd356fb01ba626dea5974fbbc062557.cat
            │       │   ├── prefiltered_func_data_mcf_conf_hp.nii.gz -> ../../../../../.git/annex/objects/p9/f8/MD5E-s43798--1a3aab41bdef47c1a75779ef26fdf175.nii.gz/MD5E-s43798--1a3aab41bdef47c1a75779ef26fdf175.nii.gz
            │       │   ├── prefiltered_func_data_mcf_conf.nii.gz -> ../../../../../.git/annex/objects/Q1/fP/MD5E-s43644--2d5d0429b2ee0fdddcdced733277751a.nii.gz/MD5E-s43644--2d5d0429b2ee0fdddcdced733277751a.nii.gz
            │       │   ├── prefiltered_func_data_mcf.par -> ../../../../../.git/annex/objects/Pg/GZ/MD5E-s32566--d1652e3ddb38bb6bf611e6fa5c5723c4.par/MD5E-s32566--d1652e3ddb38bb6bf611e6fa5c5723c4.par
            │       │   ├── prefiltered_func_data_mcf_rel_mean.rms -> ../../../../../.git/annex/objects/3P/mk/MD5E-s9--0c62fa760e910cbd6a489eda776ba0a1.rms/MD5E-s9--0c62fa760e910cbd6a489eda776ba0a1.rms
            │       │   ├── prefiltered_func_data_mcf_rel.rms -> ../../../../../.git/annex/objects/mx/p9/MD5E-s4389--a541dfb887b9b8f2c5cc47bd6a33b764.rms/MD5E-s4389--a541dfb887b9b8f2c5cc47bd6a33b764.rms
            │       │   ├── rot.png -> ../../../../../.git/annex/objects/4Z/M1/MD5E-s4225--2a3b6ca8e4886fc56fad285db2643c3a.png/MD5E-s4225--2a3b6ca8e4886fc56fad285db2643c3a.png
            │       │   └── trans.png -> ../../../../../.git/annex/objects/3z/gm/MD5E-s5657--8e1959fa13d9f243969067fb5caec5de.png/MD5E-s5657--8e1959fa13d9f243969067fb5caec5de.png
            │       ├── mean_func.nii.gz -> ../../../../.git/annex/objects/7P/77/MD5E-s553272--ef64c68bc90b329983af142d4a087288.nii.gz/MD5E-s553272--ef64c68bc90b329983af142d4a087288.nii.gz
            │       ├── reg
            │       │   ├── example_func2highres.mat -> ../../../../../.git/annex/objects/zP/p9/MD5E-s185--f59c0ce4d7f7999a069c067a29840285.mat/MD5E-s185--f59c0ce4d7f7999a069c067a29840285.mat
            │       │   ├── example_func2highres.png -> ../../../../../.git/annex/objects/v7/17/MD5E-s2062548--0ebc194d182b713a6b8c40d75f36ab9f.png/MD5E-s2062548--0ebc194d182b713a6b8c40d75f36ab9f.png
            │       │   ├── example_func2standard1.png -> ../../../../../.git/annex/objects/Jp/0K/MD5E-s319695--17ca023f22fde3e49cdfcf10041ce0da.png/MD5E-s319695--17ca023f22fde3e49cdfcf10041ce0da.png
            │       │   ├── example_func2standard.mat -> ../../../../../.git/annex/objects/W2/XF/MD5E-s187--3e8c94f30a78f33a099d8df65115975d.mat/MD5E-s187--3e8c94f30a78f33a099d8df65115975d.mat
            │       │   ├── example_func2standard.nii.gz -> ../../../../../.git/annex/objects/fg/2v/MD5E-s2757548--29e7541037791885acba38dc936cffa1.nii.gz/MD5E-s2757548--29e7541037791885acba38dc936cffa1.nii.gz
            │       │   ├── example_func2standard.png -> ../../../../../.git/annex/objects/xx/kX/MD5E-s533384--b539d1cc99d230fc8f187d583f095e83.png/MD5E-s533384--b539d1cc99d230fc8f187d583f095e83.png
            │       │   ├── example_func2standard_warp.nii.gz -> ../../../../../.git/annex/objects/fJ/jP/MD5E-s8878337--b70086c3ab91c2f3e0f714d458ac636f.nii.gz/MD5E-s8878337--b70086c3ab91c2f3e0f714d458ac636f.nii.gz
            │       │   ├── highres2standard.png -> ../../../../../.git/annex/objects/zZ/6k/MD5E-s489218--8d9950545b094b962952bcbd163928d4.png/MD5E-s489218--8d9950545b094b962952bcbd163928d4.png
            │       │   └── unwarp
            │       │       ├── EF_D_edges.gif -> ../../../../../../.git/annex/objects/ZP/m2/MD5E-s3429185--52bae5f82866786ae2f73cc477fc3a5d.gif/MD5E-s3429185--52bae5f82866786ae2f73cc477fc3a5d.gif
            │       │       ├── EF_UD_movie.gif -> ../../../../../../.git/annex/objects/Ff/J8/MD5E-s6896516--0c39208c79668f353a177a5ebe34cafb.gif/MD5E-s6896516--0c39208c79668f353a177a5ebe34cafb.gif
            │       │       ├── EF_UD_shift+mag.png -> ../../../../../../.git/annex/objects/pk/94/MD5E-s279023--603ec6e0ea418e75d208d8fe29714343.png/MD5E-s279023--603ec6e0ea418e75d208d8fe29714343.png
            │       │       ├── EF_U_edges.gif -> ../../../../../../.git/annex/objects/g8/xP/MD5E-s3467264--ffb4d63617fa8b1cadd5df8e2e8c8e24.gif/MD5E-s3467264--ffb4d63617fa8b1cadd5df8e2e8c8e24.gif
            │       │       ├── example_func_distorted2highres.png -> ../../../../../../.git/annex/objects/2J/jm/MD5E-s1949162--41d84b768223492b4c0c906819c8cd9e.png/MD5E-s1949162--41d84b768223492b4c0c906819c8cd9e.png
            │       │       ├── fieldmap2edges.png -> ../../../../../../.git/annex/objects/0w/V6/MD5E-s3371871--bb6eca0d76538099ed3b50265893a4e0.png/MD5E-s3371871--bb6eca0d76538099ed3b50265893a4e0.png
            │       │       ├── fieldmap_fout_to_T1_brain_rad.nii.gz -> ../../../../../../.git/annex/objects/vv/8Q/MD5E-s6767006--a57cc73f20883f63cae05b16cdeb7b2d.nii.gz/MD5E-s6767006--a57cc73f20883f63cae05b16cdeb7b2d.nii.gz
            │       │       ├── fmap+mag.png -> ../../../../../../.git/annex/objects/M8/GF/MD5E-s2038397--e4701e74e60a07a117ff8c70105c54a7.png/MD5E-s2038397--e4701e74e60a07a117ff8c70105c54a7.png
            │       │       ├── FM_UD_fmap_mag_brain2str.png -> ../../../../../../.git/annex/objects/Vw/fW/MD5E-s2433108--53704ebc728eeea803d3b48d33c63647.png/MD5E-s2433108--53704ebc728eeea803d3b48d33c63647.png
            │       │       └── FM_UD_sigloss+mag.png -> ../../../../../../.git/annex/objects/j0/3X/MD5E-s546163--a91bbde1e450ef314dae44729f091c6a.png/MD5E-s546163--a91bbde1e450ef314dae44729f091c6a.png
            │       ├── report.html -> ../../../../.git/annex/objects/04/12/MD5E-s910--3e3b39b50d61177aca93102689e933f2.html/MD5E-s910--3e3b39b50d61177aca93102689e933f2.html
            │       ├── report_log.html -> ../../../../.git/annex/objects/fG/G0/MD5E-s72344--37b74d02cc07000d0c8dd0f3043f92d6.html/MD5E-s72344--37b74d02cc07000d0c8dd0f3043f92d6.html
            │       ├── report_prestats.html -> ../../../../.git/annex/objects/Zz/mx/MD5E-s1475--753b9246df4197deaf7a41d365876845.html/MD5E-s1475--753b9246df4197deaf7a41d365876845.html
            │       ├── report_reg.html -> ../../../../.git/annex/objects/3P/42/MD5E-s2256--9853a45ff585f8838d9794df06eab5b1.html/MD5E-s2256--9853a45ff585f8838d9794df06eab5b1.html
            │       └── report_unwarp.html -> ../../../../.git/annex/objects/KQ/gW/MD5E-s2415--c7bf406d7acea715551ae0e35ef59b6e.html/MD5E-s2415--c7bf406d7acea715551ae0e35ef59b6e.html
            └── T1
                ├── T1_brain_mask.nii.gz -> ../../../.git/annex/objects/Gx/P7/MD5E-s539998--bcff151200027ab12c65a07384697c80.nii.gz/MD5E-s539998--bcff151200027ab12c65a07384697c80.nii.gz
                ├── T1_brain.nii.gz -> ../../../.git/annex/objects/5Q/X5/MD5E-s3819921--f44ab545040d35be8a5604d491fd73c1.nii.gz/MD5E-s3819921--f44ab545040d35be8a5604d491fd73c1.nii.gz
                ├── T1_brain_to_MNI.nii.gz -> ../../../.git/annex/objects/G7/kP/MD5E-s3862977--7ad20e5ef12ee7c992b83340c86b7032.nii.gz/MD5E-s3862977--7ad20e5ef12ee7c992b83340c86b7032.nii.gz
                ├── T1_fast
                │   ├── T1_brain_bias.nii.gz -> ../../../../.git/annex/objects/Jx/Fq/MD5E-s5952225--8153c188faa2cb009c13829e0124cc84.nii.gz/MD5E-s5952225--8153c188faa2cb009c13829e0124cc84.nii.gz
                │   ├── T1_brain_pve_0.nii.gz -> ../../../../.git/annex/objects/X2/ZJ/MD5E-s833340--9d7193d9f224aada4b5da4fb1933380e.nii.gz/MD5E-s833340--9d7193d9f224aada4b5da4fb1933380e.nii.gz
                │   ├── T1_brain_pve_1.nii.gz -> ../../../../.git/annex/objects/Kw/84/MD5E-s1555592--c229c69751bb6e51f46ee201c943d512.nii.gz/MD5E-s1555592--c229c69751bb6e51f46ee201c943d512.nii.gz
                │   ├── T1_brain_pve_2.nii.gz -> ../../../../.git/annex/objects/jz/9Z/MD5E-s921396--cacb431b800f09cb1d8536b13013000f.nii.gz/MD5E-s921396--cacb431b800f09cb1d8536b13013000f.nii.gz
                │   └── T1_brain_seg.nii.gz -> ../../../../.git/annex/objects/FQ/6w/MD5E-s412320--5b33d9627ef62db33a9fec0c0f623f59.nii.gz/MD5E-s412320--5b33d9627ef62db33a9fec0c0f623f59.nii.gz
                ├── T1_first
                │   ├── T1_first_all_fast_firstseg.nii.gz -> ../../../../.git/annex/objects/Q5/1P/MD5E-s54672--42901bf6dfbc7e9d25a88e16591c9f73.nii.gz/MD5E-s54672--42901bf6dfbc7e9d25a88e16591c9f73.nii.gz
                │   ├── T1_first-BrStem_first.bvars -> ../../../../.git/annex/objects/jk/vQ/MD5E-s1555--c6a462407f403340adfa290952a73871/MD5E-s1555--c6a462407f403340adfa290952a73871
                │   ├── T1_first-BrStem_first.vtk -> ../../../../.git/annex/objects/xK/fW/MD5E-s32580--91ee8d365c67e30255605b08ba7f1ea3.vtk/MD5E-s32580--91ee8d365c67e30255605b08ba7f1ea3.vtk
                │   ├── T1_first-L_Accu_first.bvars -> ../../../../.git/annex/objects/JK/xj/MD5E-s1555--103cfa0f07c4c73b38989ffaed8dc647/MD5E-s1555--103cfa0f07c4c73b38989ffaed8dc647
                │   ├── T1_first-L_Accu_first.vtk -> ../../../../.git/annex/objects/20/qf/MD5E-s32614--4f7472bbb644438306679196a8253784.vtk/MD5E-s32614--4f7472bbb644438306679196a8253784.vtk
                │   ├── T1_first-L_Amyg_first.bvars -> ../../../../.git/annex/objects/QX/PX/MD5E-s1563--0d4eb8067bba528ebccb86749a178c3f/MD5E-s1563--0d4eb8067bba528ebccb86749a178c3f
                │   ├── T1_first-L_Amyg_first.vtk -> ../../../../.git/annex/objects/WX/94/MD5E-s32620--523fff20ac3c565553c30fc97af3d78f.vtk/MD5E-s32620--523fff20ac3c565553c30fc97af3d78f.vtk
                │   ├── T1_first-L_Caud_first.bvars -> ../../../../.git/annex/objects/MW/V2/MD5E-s1563--62bc6953894bfe640e6342097d7e0b24/MD5E-s1563--62bc6953894bfe640e6342097d7e0b24
                │   ├── T1_first-L_Caud_first.vtk -> ../../../../.git/annex/objects/4m/1j/MD5E-s49544--1e0a78cea67d0987c5e401a0a770a152.vtk/MD5E-s49544--1e0a78cea67d0987c5e401a0a770a152.vtk
                │   ├── T1_first-L_Hipp_first.bvars -> ../../../../.git/annex/objects/pq/0x/MD5E-s1563--82479b46cefacb21ac14b1aedc9b8ce4/MD5E-s1563--82479b46cefacb21ac14b1aedc9b8ce4
                │   ├── T1_first-L_Hipp_first.vtk -> ../../../../.git/annex/objects/jj/qX/MD5E-s37224--5eaad87fa8ec5918e06236b71d8b7078.vtk/MD5E-s37224--5eaad87fa8ec5918e06236b71d8b7078.vtk
                │   ├── T1_first-L_Pall_first.bvars -> ../../../../.git/annex/objects/j9/8f/MD5E-s1561--b4c3c5ac646008bf6f485093cffc1cbc/MD5E-s1561--b4c3c5ac646008bf6f485093cffc1cbc
                │   ├── T1_first-L_Pall_first.vtk -> ../../../../.git/annex/objects/8z/PJ/MD5E-s32582--d32de3b9b9bfa791d075b133d3ff87a2.vtk/MD5E-s32582--d32de3b9b9bfa791d075b133d3ff87a2.vtk
                │   ├── T1_first-L_Puta_first.bvars -> ../../../../.git/annex/objects/Z0/kf/MD5E-s1561--b6d28dd6090e271626453b9e173a93bd/MD5E-s1561--b6d28dd6090e271626453b9e173a93bd
                │   ├── T1_first-L_Puta_first.vtk -> ../../../../.git/annex/objects/XW/5F/MD5E-s32602--46d5c5dafd5ffd1086ef5cf0bce37950.vtk/MD5E-s32602--46d5c5dafd5ffd1086ef5cf0bce37950.vtk
                │   ├── T1_first-L_Thal_first.bvars -> ../../../../.git/annex/objects/jK/fP/MD5E-s1561--b1d9daa8ffdbdd734df2529c707d9169/MD5E-s1561--b1d9daa8ffdbdd734df2529c707d9169
                │   ├── T1_first-L_Thal_first.vtk -> ../../../../.git/annex/objects/jG/47/MD5E-s32593--a4f9c5f963122eda47220c1af667483a.vtk/MD5E-s32593--a4f9c5f963122eda47220c1af667483a.vtk
                │   ├── T1_first-R_Accu_first.bvars -> ../../../../.git/annex/objects/Xm/Xq/MD5E-s1555--d3a235caa580934f00e2d2dd2d733ca4/MD5E-s1555--d3a235caa580934f00e2d2dd2d733ca4
                │   ├── T1_first-R_Accu_first.vtk -> ../../../../.git/annex/objects/0J/k2/MD5E-s32604--3f4485c8b8c662ff995d67f4307aaa9c.vtk/MD5E-s32604--3f4485c8b8c662ff995d67f4307aaa9c.vtk
                │   ├── T1_first-R_Amyg_first.bvars -> ../../../../.git/annex/objects/Xv/Gg/MD5E-s1563--5f15072c8946d1e28c63f5436ae217ed/MD5E-s1563--5f15072c8946d1e28c63f5436ae217ed
                │   ├── T1_first-R_Amyg_first.vtk -> ../../../../.git/annex/objects/jQ/mm/MD5E-s32612--272407084716c891b1da3fbbf025f960.vtk/MD5E-s32612--272407084716c891b1da3fbbf025f960.vtk
                │   ├── T1_first-R_Caud_first.bvars -> ../../../../.git/annex/objects/4G/z2/MD5E-s1563--462573fd1aed8118a56746ea9761a7a4/MD5E-s1563--462573fd1aed8118a56746ea9761a7a4
                │   ├── T1_first-R_Caud_first.vtk -> ../../../../.git/annex/objects/xf/63/MD5E-s54989--7c24733d70a35436aa3be836beccbbb2.vtk/MD5E-s54989--7c24733d70a35436aa3be836beccbbb2.vtk
                │   ├── T1_first-R_Hipp_first.bvars -> ../../../../.git/annex/objects/02/MQ/MD5E-s1563--719ce159c5e2e25a187b4209142801e0/MD5E-s1563--719ce159c5e2e25a187b4209142801e0
                │   ├── T1_first-R_Hipp_first.vtk -> ../../../../.git/annex/objects/Gg/Xj/MD5E-s33706--c209a1f3ed1bb1cdcc13287b190288ba.vtk/MD5E-s33706--c209a1f3ed1bb1cdcc13287b190288ba.vtk
                │   ├── T1_first-R_Pall_first.bvars -> ../../../../.git/annex/objects/PV/MF/MD5E-s1561--4ff3ebb4caa8201285e1282fa2f7d07e/MD5E-s1561--4ff3ebb4caa8201285e1282fa2f7d07e
                │   ├── T1_first-R_Pall_first.vtk -> ../../../../.git/annex/objects/zw/5V/MD5E-s32597--ec7642786b38a7ecdc7d9380c7e99611.vtk/MD5E-s32597--ec7642786b38a7ecdc7d9380c7e99611.vtk
                │   ├── T1_first-R_Puta_first.bvars -> ../../../../.git/annex/objects/q0/0v/MD5E-s1561--1a9eb3a675d160f73eefd6e689ed9a8f/MD5E-s1561--1a9eb3a675d160f73eefd6e689ed9a8f
                │   ├── T1_first-R_Puta_first.vtk -> ../../../../.git/annex/objects/Mq/kX/MD5E-s32628--1d2f4344df2c6c75a6d5b2ff010e5cfe.vtk/MD5E-s32628--1d2f4344df2c6c75a6d5b2ff010e5cfe.vtk
                │   ├── T1_first-R_Thal_first.bvars -> ../../../../.git/annex/objects/2x/j2/MD5E-s1561--081cb66efb9573a491b74b4d848b68e6/MD5E-s1561--081cb66efb9573a491b74b4d848b68e6
                │   └── T1_first-R_Thal_first.vtk -> ../../../../.git/annex/objects/G7/5p/MD5E-s32608--3a981d0920d30d989911ab700fbe7be8.vtk/MD5E-s32608--3a981d0920d30d989911ab700fbe7be8.vtk
                ├── T1_orig_defaced.nii.gz -> ../../../.git/annex/objects/k5/Wz/MD5E-s20284968--5468c35d0dd550615764326d5ac10ab1.nii.gz/MD5E-s20284968--5468c35d0dd550615764326d5ac10ab1.nii.gz
                ├── T1_unbiased_brain.nii.gz -> ../../../.git/annex/objects/p9/33/MD5E-s6410788--5a9b65be9947cab036f35ad18e96eda8.nii.gz/MD5E-s6410788--5a9b65be9947cab036f35ad18e96eda8.nii.gz
                └── transforms
                    ├── T1_to_MNI_linear.mat -> ../../../../.git/annex/objects/4k/J6/MD5E-s189--c6abbec22f6c11eecb928e5544eedfc6.mat/MD5E-s189--c6abbec22f6c11eecb928e5544eedfc6.mat
                    └── T1_to_MNI_warp_coef.nii.gz -> ../../../../.git/annex/objects/px/x9/MD5E-s118638--591edf07be6feff791ca0c16861283c1.nii.gz/MD5E-s118638--591edf07be6feff791ca0c16861283c1.nii.gz

Thank you,

loj commented 2 years ago

Hey, whether or not json files are associated with the nifti images is dependent on whether or not they are provided by the UK Biobank.

datalad-ukbiobank simply takes the downloaded zip files, extracts the content, and then converts the extracted content to a BIDS(-like) layout. If you want to view the extracted files in the original layout provided by the UK Biobank, you can checkout the incoming-native branch.

ltetrel commented 2 years ago

Thanks for the reply.

This participant was indeed lacking the json file sin the archive. I think it it because we have outdated version for some of them. I will close this issue since this is related to our data