├── .datalad ├── config └── .gitattributes ├── task-rhymejudgment_bold.json ├── code ├── nda-stuff │ ├── .gitattributes │ ├── guid-mapping.txt │ ├── image03.txt │ └── shell-history └── prep4nda.sh ├── sub-01 ├── sub-01_scans.tsv └── anat │ ├── sub-01_T1w.nii.gz │ └── sub-01_inplaneT2.nii.gz ├── sub-02 ├── sub-02_scans.tsv └── anat │ ├── sub-02_T1w.nii.gz │ └── sub-02_inplaneT2.nii.gz ├── sub-03 ├── sub-03_scans.tsv └── anat │ ├── sub-03_T1w.nii.gz │ └── sub-03_inplaneT2.nii.gz ├── .gitmodules ├── participants.tsv ├── .gitattributes ├── CHANGES ├── dataset_description.json └── README /.datalad/config: -------------------------------------------------------------------------------- 1 | [datalad "dataset"] 2 | id = 9040fae2-8704-11e8-aff3-0242ac12000c 3 | -------------------------------------------------------------------------------- /task-rhymejudgment_bold.json: -------------------------------------------------------------------------------- 1 | { 2 | "RepetitionTime": 2.0, 3 | "TaskName": "rhyme judgment" 4 | } -------------------------------------------------------------------------------- /code/nda-stuff/.gitattributes: -------------------------------------------------------------------------------- 1 | * annex.largefiles=anything 2 | .* annex.largefiles=nothing 3 | shell-history annex.largefiles=nothing 4 | -------------------------------------------------------------------------------- /sub-01/sub-01_scans.tsv: -------------------------------------------------------------------------------- 1 | filename acq_time 2 | anat/sub-01_inplaneT2.nii.gz 2018-09-10T12:22:18 3 | anat/sub-01_T1w.nii.gz 2018-09-10T12:22:18 4 | -------------------------------------------------------------------------------- /sub-02/sub-02_scans.tsv: -------------------------------------------------------------------------------- 1 | filename acq_time 2 | anat/sub-02_inplaneT2.nii.gz 2018-09-10T12:22:18 3 | anat/sub-02_T1w.nii.gz 2018-09-10T12:22:18 4 | -------------------------------------------------------------------------------- /sub-03/sub-03_scans.tsv: -------------------------------------------------------------------------------- 1 | filename acq_time 2 | anat/sub-03_inplaneT2.nii.gz 2018-09-10T12:22:18 3 | anat/sub-03_T1w.nii.gz 2018-09-10T12:22:18 4 | -------------------------------------------------------------------------------- /code/nda-stuff/guid-mapping.txt: -------------------------------------------------------------------------------- 1 | ../../.git/annex/objects/X4/vX/MD5E-s33--0402c473227c3ace60d3aeac03932d6a.txt/MD5E-s33--0402c473227c3ace60d3aeac03932d6a.txt -------------------------------------------------------------------------------- /code/nda-stuff/image03.txt: -------------------------------------------------------------------------------- 1 | ../../.git/annex/objects/2k/Mk/MD5E-s4177--f7efc828bb9ebe727a3d519cd75a1d94.txt/MD5E-s4177--f7efc828bb9ebe727a3d519cd75a1d94.txt -------------------------------------------------------------------------------- /.datalad/.gitattributes: -------------------------------------------------------------------------------- 1 | config annex.largefiles=nothing 2 | metadata/aggregate* annex.largefiles=nothing 3 | metadata/objects/** annex.largefiles=(largerthan=20kb) 4 | -------------------------------------------------------------------------------- /sub-01/anat/sub-01_T1w.nii.gz: -------------------------------------------------------------------------------- 1 | ../../.git/annex/objects/jJ/2v/MD5E-s5712417--0d1e0a7ff7063250404f45a955a66203.nii.gz/MD5E-s5712417--0d1e0a7ff7063250404f45a955a66203.nii.gz -------------------------------------------------------------------------------- /sub-01/anat/sub-01_inplaneT2.nii.gz: -------------------------------------------------------------------------------- 1 | ../../.git/annex/objects/J3/q7/MD5E-s664614--0f8bc47f9c3047b340abfcd3ce1fb021.nii.gz/MD5E-s664614--0f8bc47f9c3047b340abfcd3ce1fb021.nii.gz -------------------------------------------------------------------------------- /sub-02/anat/sub-02_T1w.nii.gz: -------------------------------------------------------------------------------- 1 | ../../.git/annex/objects/5g/pJ/MD5E-s5907060--89189d319055e674f76f1524706bac81.nii.gz/MD5E-s5907060--89189d319055e674f76f1524706bac81.nii.gz -------------------------------------------------------------------------------- /sub-02/anat/sub-02_inplaneT2.nii.gz: -------------------------------------------------------------------------------- 1 | ../../.git/annex/objects/99/p1/MD5E-s682007--f368aa44caf7bd14238963116d04c70e.nii.gz/MD5E-s682007--f368aa44caf7bd14238963116d04c70e.nii.gz -------------------------------------------------------------------------------- /sub-03/anat/sub-03_T1w.nii.gz: -------------------------------------------------------------------------------- 1 | ../../.git/annex/objects/MP/Jf/MD5E-s5635821--b0bca1dcc0a53e78ba2c7e857e4e5321.nii.gz/MD5E-s5635821--b0bca1dcc0a53e78ba2c7e857e4e5321.nii.gz -------------------------------------------------------------------------------- /sub-03/anat/sub-03_inplaneT2.nii.gz: -------------------------------------------------------------------------------- 1 | ../../.git/annex/objects/1F/xk/MD5E-s657299--96e547595578baf28a63348ddbd672e2.nii.gz/MD5E-s657299--96e547595578baf28a63348ddbd672e2.nii.gz -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- 1 | [submodule "code/bids2nda"] 2 | path = code/bids2nda 3 | url = https://github.com/bids-standard/bids2nda 4 | datalad-url = https://github.com/bids-standard/bids2nda 5 | -------------------------------------------------------------------------------- /code/prep4nda.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | git rm -rf sub-1* sub-0[4-9] # remove subj I don't want to share 4 | git rm -r sub*/func # remove functional I don't want to share 5 | git rm -r derivatives 6 | -------------------------------------------------------------------------------- /participants.tsv: -------------------------------------------------------------------------------- 1 | participant_id sex age 2 | sub-01 M 25 3 | sub-02 M 18 4 | sub-03 F 22 5 | sub-04 F 25 6 | sub-05 M 22 7 | sub-06 M 38 8 | sub-07 M 36 9 | sub-08 M 19 10 | sub-09 M 20 11 | sub-10 F 19 12 | sub-11 F 21 13 | sub-12 M 19 14 | sub-13 F 29 15 | -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | * annex.backend=MD5E 2 | **/.git* annex.largefiles=nothing 3 | *.tsv annex.largefiles=nothing 4 | *.json annex.largefiles=nothing 5 | *.bvec annex.largefiles=nothing 6 | *.bval annex.largefiles=nothing 7 | README annex.largefiles=nothing 8 | CHANGES annex.largefiles=nothing 9 | .bidsignore annex.largefiles=nothing 10 | -------------------------------------------------------------------------------- /CHANGES: -------------------------------------------------------------------------------- 1 | 2.0.1 2016-09-30 2 | 3 | - added authors to dataset_description.json 4 | 5 | 2.0.0 2016-09-28 6 | 7 | - converted to BIDS format from openfmri format 8 | 9 | 1.0.1 2016-02-18 10 | 11 | - Updated orientation information in nifti headers for improved left-right determination 12 | 13 | 14 | 1.0.0 2020-05-14 15 | - Creating DOI 16 | -------------------------------------------------------------------------------- /dataset_description.json: -------------------------------------------------------------------------------- 1 | { 2 | "Name": "Rhyme judgment", 3 | "License": "CC0", 4 | "Authors": [ 5 | "Xue, G.", 6 | "Russell A. Poldrack" 7 | ], 8 | "Acknowledgements": "", 9 | "HowToAcknowledge": "", 10 | "Funding": "", 11 | "ReferencesAndLinks": [], 12 | "DatasetDOI": "10.18112/openneuro.ds000003.v1.0.0", 13 | "BIDSVersion": "1.0.0" 14 | } -------------------------------------------------------------------------------- /README: -------------------------------------------------------------------------------- 1 | This dataset was obtained from the OpenfMRI project (http://www.openfmri.org). 2 | Accession #: ds003 3 | Description: Rhyme judgment 4 | 5 | This is a very trimmed dataset for bids2nda demo on how to use DataLad 6 | efficiently to accomplish the mission of trimming dataset for use with bids2nda tool. 7 | `code/nda-stuff/shell-history` file contains an unedited shell history listing 8 | all commands (including errorneous) which were done for this repo until it got shared etc. 9 | 10 | Release history: 11 | 07/14/2023: modified for bids2nda demo by @yarikoptic 12 | 10/06/2011: initial release 13 | 3/21/2013: Updated release with QA information 14 | 2/18/2016: Updated orientation information in nifti headers for improved left-right determination 15 | 16 | This dataset is made available under the Public Domain Dedication and License 17 | v1.0, whose full text can be found at 18 | http://www.opendatacommons.org/licenses/pddl/1.0/. 19 | We hope that all users will follow the ODC Attribution/Share-Alike 20 | Community Norms (http://www.opendatacommons.org/norms/odc-by-sa/); 21 | in particular, while not legally required, we hope that all users 22 | of the data will acknowledge the OpenfMRI project and NSF Grant 23 | OCI-1131441 (R. Poldrack, PI) in any publications. 24 | -------------------------------------------------------------------------------- /code/nda-stuff/shell-history: -------------------------------------------------------------------------------- 1 | datalad clone ///openneuro/ds000003 2 | cd ds000003 3 | git checkout -b nda 4 | ls sub-01 5 | mkdir code 6 | vim code/prep4nda.sh 7 | git add code/prep4nda.sh 8 | git commit -m 'add my precious script to remove stuff to not be going to NDA' code/prep4nda.sh 9 | ls -l code/prep4nda.sh 10 | code/prep4nda.sh 11 | vim code/prep4nda.sh 12 | git commit --amend code/prep4nda.sh 13 | git status 14 | git reset --hard 15 | code/prep4nda.sh 16 | git status 17 | ls 18 | ls derivatives 19 | vim code/prep4nda.sh 20 | git commit --amend code/prep4nda.sh 21 | git reset --hard 22 | git commit --amend code/prep4nda.sh 23 | code/prep4nda.sh 24 | ls 25 | ls sub-0* 26 | ls sub-0*/anat 27 | git reset --hard 28 | datalad run -m "Trim dataset to only stuff I want to upload to NDA" code/prep4nda.sh 29 | ls 30 | git show 31 | ls 32 | git co - 33 | ls 34 | git alias co 35 | git config alias.co 36 | git checkout - 37 | ls 38 | git checkout - 39 | ls 40 | git checkout - 41 | datalad get sub-0 42 | datalad get sub-0* 43 | datalad clone -d . --source https://github.com/bids-standard/bids2nda code/bids2nda 44 | datalad clone -d . https://github.com/bids-standard/bids2nda code/bids2nda 45 | datalad subdatasets 46 | ls -l code/bids2nda 47 | datalad drop code/bids2nda 48 | ls -l code/bids2nda 49 | datalad uninstall code/bids2nda 50 | ls -l code/bids2nda 51 | datalad install code/bids2nda 52 | py=3; d=venv; python$py -m venv $d && source $d/bin/activate && pip install -e code/bids2nda 53 | bids2nda 54 | git status 55 | echo venv >> .git/info/exclude 56 | git status 57 | ls 58 | bids2nda 59 | vim participants.tsv 60 | mkdir code/nda-stuff 61 | vim code/nda-stuff/guid-mapping.txt 62 | vim code/bids2nda/README.md 63 | fg 64 | vim code/nda-stuff/guid-mapping.txt 65 | vim code/nda-stuff/.gitattributes 66 | git add code/nda-stuff/.gitattributes 67 | ls -ld code/nda-stuff/.gitattributes 68 | git annex add code/nda-stuff/guid-mapping.txt 69 | ls -l code/nda-stuff/guid-mapping.txt 70 | bids2nda 71 | echo bids2nda . code/nda-stuff/guid-mapping.txt code/nda-stuff 72 | git status 73 | git commit -m 'Our NDA GUID mapping file + instructions to not commit to git in that folder' 74 | bids2nda . code/nda-stuff/guid-mapping.txt code/nda-stuff 75 | cd ~/datalad/dbic 76 | d+ 77 | ls 78 | datalad install . 79 | ls 80 | cd QA/ 81 | datalad install . 82 | ls 83 | cd sub-qa 84 | cd ses-20180910/ 85 | ls 86 | cd anat 87 | ls 88 | cd .. 89 | ls 90 | echo $PWD/sub-qa_ses-20180910_scans.tsv 91 | cd -6 92 | cd sub-01 93 | cp /home/yoh/datalad/dbic/QA/sub-qa/ses-20180910/sub-qa_ses-20180910_scans.tsv sub-01_scans.tsv 94 | vim sub-01_scans.tsv 95 | for f in anat/*nii.gz; do echo -e "$f\t2018-09-10T12:22:18" >> sub-01_scans.tsv; done 96 | ls -l 97 | cp sub-01_scans.tsv ../sub-02 98 | cd ../sub-02 99 | mv sub-01_scans.tsv sub-02_scans.tsv 100 | vim sub-02_scans.tsv 101 | for f in anat/*nii.gz; do echo -e "$f\t2018-09-10T12:22:18" >> sub-02_scans.tsv; done 102 | vim sub-02_scans.tsv 103 | cd - 104 | vim sub-01_scans.tsv 105 | cd .. 106 | git status 107 | datalad save -m "Generate fake scans files for demonstration purposes" 108 | bids2nda . code/nda-stuff/guid-mapping.txt code/nda-stuff 109 | vim /mnt/btrfs/scrap/tmp/ds000003/code/bids2nda/bids2nda/main.py 110 | find sub-0* 111 | ls 112 | tree sub-0* 113 | vim /mnt/btrfs/scrap/tmp/ds000003/code/bids2nda/bids2nda/main.py 114 | fg 115 | bids2nda . code/nda-stuff/guid-mapping.txt code/nda-stuff 116 | cat code/nda-stuff/image03.txt 117 | cd - 118 | cd ../code/nda-stuff 119 | git diff 120 | cd ../bids2nda 121 | git checkout -b add-inplaneT2 122 | git diff 123 | git commit -m 'Add mapping of inplaneT2 to MR structural (T2)' -a 124 | ghsendpr origin 125 | cd ../../ 126 | git status 127 | git commit -m 'We need to use patched (for inlineT2 support) bids2nda' code/bids2nda 128 | rm code/nda-stuff/image03.txt 129 | datalad run -m "Produce image03.txt for submission to NDA" --input sub-* --input code/nda-stuff/guid-mapping.txt --output code/nda-stuff bids2nda . code/nda-stuff/guid-mapping.txt code/nda-stuff 130 | datalad run -m "Produce image03.txt for submission to NDA" --input 'sub-*' --input code/nda-stuff/guid-mapping.txt --output code/nda-stuff bids2nda . code/nda-stuff/guid-mapping.txt code/nda-stuff 131 | top 132 | ls -l code/nda-stuff 133 | git log 134 | cd ../ 135 | datalad clone ds000003 ds000003-redo 136 | cd ds000003-redo 137 | git show 138 | datalad rerun 139 | cd - 140 | cd ds000003 141 | vim code/prep4nda.sh 142 | git diff 143 | git commit -m 'now we want to get sub-03 into nda' -a 144 | git checkout master 145 | ls 146 | tar -czvf sub-03.tgz sub-03 147 | git checkout - 148 | tar -xzvf sub-03.tgz 149 | rm sub-03.tgz 150 | datalad save -m "Added sub-03 from master via a tarball" 151 | git log 152 | datalad rerun 98881137c6d60c8937eb3d82920b5d0aad349e13 153 | git status 154 | git show --stat 155 | cp sub-02/sub-02_scans.tsv sub-03/sub-3_scans.tsv 156 | vim sub-03/sub-3_scans.tsv 157 | git annex unlock code/nda-stuff/guid-mapping.txt 158 | vim code/nda-stuff/guid-mapping.txt 159 | git status 160 | datalad save -m "created fake scans file for sub03 and added into guid mapping" 161 | git log 162 | datalad rerun 8b58f1ffbb1cb99fb434f1c765ddd0d71ab3725b 163 | ls sub-03 164 | datalad save -m "fix scans file" git mv sub-3_scans.tsv sub-03_scans.tsv 165 | git status 166 | ls sub-03_scans.tsv 167 | cd sub-03 168 | datalad save -m "fix scans file" git mv sub-3_scans.tsv sub-03_scans.tsv 169 | ls 170 | datalad save -m "fix scans file" mv sub-3_scans.tsv sub-03_scans.tsv 171 | ls 172 | datalad run -m "fix scans file" mv sub-3_scans.tsv sub-03_scans.tsv 173 | ls 174 | cd .. 175 | datalad rerun 8b58f1ffbb1cb99fb434f1c765ddd0d71ab3725b 176 | cat code/nda-stuff/image03.txt 177 | --------------------------------------------------------------------------------