When I use the command line client on a dataset it exits with 0 and no output (not eve

command line client silently fails to read .nii.gz files,about bids-standard/bids-validator

Comments (13)

constellates commented on July 19, 2024

I'm not able to reproduce this. Are you experiencing this on a particular dataset. I just tested in node v5.0.0 and ds114 as well as a few others on the current master. If I log the header after the following line I can see the full header contents of each nifti https://github.com/INCF/bids-validator/blob/master/validators/bids.js#L171 .

from bids-validator.

chrisgorgo commented on July 19, 2024

My debugger does not even get into this line. Here is everything I tested:

orange:bids-validator filo$ git checkout master
Already on 'master'
orange:bids-validator filo$ git pull upstream master
From github.com:INCF/bids-validator
 * branch            master     -> FETCH_HEAD
Already up-to-date.
orange:bids-validator filo$ git diff
orange:bids-validator filo$ node --version
v4.2.4
orange:bids-validator filo$ bin/bids-validator ../BIDS-examples/ds114
orange:bids-validator filo$ brew uninstall node4-lts && brew install node
Uninstalling /usr/local/Cellar/node4-lts/4.2.4... (2,825 files, 29.1M)
Warning: node-5.3.0 already installed, it's just not linked
orange:bids-validator filo$ brew link node
Linking /usr/local/Cellar/node/5.3.0... 7 symlinks created
orange:bids-validator filo$ node --version
v5.3.0
orange:bids-validator filo$ bin/bids-validator ../BIDS-examples/ds114
orange:bids-validator filo$ git checkout 0910
Note: checking out '0910'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b <new-branch-name>

HEAD is now at 0910b2f... fixed version number missed in rebase
orange:bids-validator filo$ bin/bids-validator ../BIDS-examples/ds114
orange:bids-validator filo$ brew uninstall node
Uninstalling /usr/local/Cellar/node/5.3.0... (2,827 files, 29.4M)
node 5.1.0, 5.2.0 are still installed.
Remove them all with `brew uninstall --force node`.
orange:bids-validator filo$ brew install node4-lts
==> Installing node4-lts from homebrew/versions
==> Downloading https://homebrew.bintray.com/bottles-versions/node4-lts-4.2.4.el_capitan.bottle.tar.gz
Already downloaded: /Library/Caches/Homebrew/node4-lts-4.2.4.el_capitan.bottle.tar.gz
==> Pouring node4-lts-4.2.4.el_capitan.bottle.tar.gz
==> Caveats
Bash completion has been installed to:
  /usr/local/etc/bash_completion.d
==> Summary
🍺  /usr/local/Cellar/node4-lts/4.2.4: 2,825 files, 29.1M
orange:bids-validator filo$ node --version
v4.2.4
orange:bids-validator filo$ bin/bids-validator ../BIDS-examples/ds114
    1: You should should define 'EchoTime' for this file. If you don't provide this information field map correction will not be possible. (code: 6)
        /sub-01/ses-retest/dwi/sub-01_ses-retest_dwi.nii.gz
        /sub-01/ses-test/dwi/sub-01_ses-test_dwi.nii.gz
        /sub-02/ses-retest/dwi/sub-02_ses-retest_dwi.nii.gz
        /sub-02/ses-test/dwi/sub-02_ses-test_dwi.nii.gz
        /sub-03/ses-retest/dwi/sub-03_ses-retest_dwi.nii.gz
        /sub-03/ses-test/dwi/sub-03_ses-test_dwi.nii.gz
        /sub-04/ses-retest/dwi/sub-04_ses-retest_dwi.nii.gz
        /sub-04/ses-test/dwi/sub-04_ses-test_dwi.nii.gz
        /sub-05/ses-retest/dwi/sub-05_ses-retest_dwi.nii.gz
        /sub-05/ses-test/dwi/sub-05_ses-test_dwi.nii.gz
        /sub-06/ses-retest/dwi/sub-06_ses-retest_dwi.nii.gz
        /sub-06/ses-test/dwi/sub-06_ses-test_dwi.nii.gz
        /sub-07/ses-retest/dwi/sub-07_ses-retest_dwi.nii.gz
        /sub-07/ses-test/dwi/sub-07_ses-test_dwi.nii.gz
        /sub-08/ses-retest/dwi/sub-08_ses-retest_dwi.nii.gz
        /sub-08/ses-test/dwi/sub-08_ses-test_dwi.nii.gz
        /sub-09/ses-retest/dwi/sub-09_ses-retest_dwi.nii.gz
        /sub-09/ses-test/dwi/sub-09_ses-test_dwi.nii.gz
        /sub-10/ses-retest/dwi/sub-10_ses-retest_dwi.nii.gz
        /sub-10/ses-test/dwi/sub-10_ses-test_dwi.nii.gz

    2: You should should define 'PhaseEncodingDirection' for this file. If you don't provide this information field map correction will not be possible. (code: 7)
        /sub-01/ses-retest/dwi/sub-01_ses-retest_dwi.nii.gz
        /sub-01/ses-retest/func/sub-01_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-01/ses-retest/func/sub-01_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-01/ses-retest/func/sub-01_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-01/ses-retest/func/sub-01_ses-retest_task-linebisection_bold.nii.gz
        /sub-01/ses-retest/func/sub-01_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-01/ses-test/func/sub-01_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-01/ses-test/dwi/sub-01_ses-test_dwi.nii.gz
        /sub-01/ses-test/func/sub-01_ses-test_task-linebisection_bold.nii.gz
        /sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-01/ses-test/func/sub-01_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-01/ses-test/func/sub-01_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-02/ses-retest/dwi/sub-02_ses-retest_dwi.nii.gz
        /sub-02/ses-retest/func/sub-02_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-02/ses-retest/func/sub-02_ses-retest_task-linebisection_bold.nii.gz
        /sub-02/ses-retest/func/sub-02_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-02/ses-retest/func/sub-02_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-02/ses-retest/func/sub-02_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-02/ses-test/dwi/sub-02_ses-test_dwi.nii.gz
        /sub-02/ses-test/func/sub-02_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-02/ses-test/func/sub-02_ses-test_task-linebisection_bold.nii.gz
        /sub-02/ses-test/func/sub-02_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-02/ses-test/func/sub-02_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-02/ses-test/func/sub-02_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-03/ses-retest/dwi/sub-03_ses-retest_dwi.nii.gz
        /sub-03/ses-retest/func/sub-03_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz
        /sub-03/ses-retest/func/sub-03_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-03/ses-retest/func/sub-03_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-03/ses-retest/func/sub-03_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-03/ses-test/func/sub-03_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-03/ses-test/dwi/sub-03_ses-test_dwi.nii.gz
        /sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz
        /sub-03/ses-test/func/sub-03_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-03/ses-test/func/sub-03_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-03/ses-test/func/sub-03_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-04/ses-retest/func/sub-04_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-04/ses-retest/dwi/sub-04_ses-retest_dwi.nii.gz
        /sub-04/ses-retest/func/sub-04_ses-retest_task-linebisection_bold.nii.gz
        /sub-04/ses-retest/func/sub-04_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-04/ses-retest/func/sub-04_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-04/ses-retest/func/sub-04_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-04/ses-test/dwi/sub-04_ses-test_dwi.nii.gz
        /sub-04/ses-test/func/sub-04_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-04/ses-test/func/sub-04_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-04/ses-test/func/sub-04_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-04/ses-test/func/sub-04_ses-test_task-linebisection_bold.nii.gz
        /sub-04/ses-test/func/sub-04_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-05/ses-retest/dwi/sub-05_ses-retest_dwi.nii.gz
        /sub-05/ses-retest/func/sub-05_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-05/ses-retest/func/sub-05_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-05/ses-retest/func/sub-05_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-05/ses-retest/func/sub-05_ses-retest_task-linebisection_bold.nii.gz
        /sub-05/ses-retest/func/sub-05_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-05/ses-test/dwi/sub-05_ses-test_dwi.nii.gz
        /sub-05/ses-test/func/sub-05_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-05/ses-test/func/sub-05_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-05/ses-test/func/sub-05_ses-test_task-linebisection_bold.nii.gz
        /sub-05/ses-test/func/sub-05_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-05/ses-test/func/sub-05_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-06/ses-retest/func/sub-06_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-06/ses-retest/dwi/sub-06_ses-retest_dwi.nii.gz
        /sub-06/ses-retest/func/sub-06_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-06/ses-retest/func/sub-06_ses-retest_task-linebisection_bold.nii.gz
        /sub-06/ses-retest/func/sub-06_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-06/ses-retest/func/sub-06_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-06/ses-test/dwi/sub-06_ses-test_dwi.nii.gz
        /sub-06/ses-test/func/sub-06_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-06/ses-test/func/sub-06_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-06/ses-test/func/sub-06_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-06/ses-test/func/sub-06_ses-test_task-linebisection_bold.nii.gz
        /sub-06/ses-test/func/sub-06_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-07/ses-retest/dwi/sub-07_ses-retest_dwi.nii.gz
        /sub-07/ses-retest/func/sub-07_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-07/ses-retest/func/sub-07_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-07/ses-retest/func/sub-07_ses-retest_task-linebisection_bold.nii.gz
        /sub-07/ses-retest/func/sub-07_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-07/ses-retest/func/sub-07_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-07/ses-test/dwi/sub-07_ses-test_dwi.nii.gz
        /sub-07/ses-test/func/sub-07_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-07/ses-test/func/sub-07_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-07/ses-test/func/sub-07_ses-test_task-linebisection_bold.nii.gz
        /sub-07/ses-test/func/sub-07_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-07/ses-test/func/sub-07_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-08/ses-retest/dwi/sub-08_ses-retest_dwi.nii.gz
        /sub-08/ses-retest/func/sub-08_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-08/ses-retest/func/sub-08_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-08/ses-retest/func/sub-08_ses-retest_task-linebisection_bold.nii.gz
        /sub-08/ses-retest/func/sub-08_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-08/ses-retest/func/sub-08_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-08/ses-test/dwi/sub-08_ses-test_dwi.nii.gz
        /sub-08/ses-test/func/sub-08_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-08/ses-test/func/sub-08_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-08/ses-test/func/sub-08_ses-test_task-linebisection_bold.nii.gz
        /sub-08/ses-test/func/sub-08_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-08/ses-test/func/sub-08_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-09/ses-retest/dwi/sub-09_ses-retest_dwi.nii.gz
        /sub-09/ses-retest/func/sub-09_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-09/ses-retest/func/sub-09_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-09/ses-retest/func/sub-09_ses-retest_task-linebisection_bold.nii.gz
        /sub-09/ses-retest/func/sub-09_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-09/ses-retest/func/sub-09_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-09/ses-test/dwi/sub-09_ses-test_dwi.nii.gz
        /sub-09/ses-test/func/sub-09_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-09/ses-test/func/sub-09_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-09/ses-test/func/sub-09_ses-test_task-linebisection_bold.nii.gz
        /sub-09/ses-test/func/sub-09_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-09/ses-test/func/sub-09_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-10/ses-retest/dwi/sub-10_ses-retest_dwi.nii.gz
        /sub-10/ses-retest/func/sub-10_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-10/ses-retest/func/sub-10_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-10/ses-retest/func/sub-10_ses-retest_task-linebisection_bold.nii.gz
        /sub-10/ses-retest/func/sub-10_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-10/ses-retest/func/sub-10_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-10/ses-test/func/sub-10_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-10/ses-test/dwi/sub-10_ses-test_dwi.nii.gz
        /sub-10/ses-test/func/sub-10_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-10/ses-test/func/sub-10_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-10/ses-test/func/sub-10_ses-test_task-linebisection_bold.nii.gz
        /sub-10/ses-test/func/sub-10_ses-test_task-overtwordrepetition_bold.nii.gz

    3: You should should define 'EffectiveEchoSpacing' for this file. If you don't provide this information field map correction will not be possible. (code: 8)
        /sub-01/ses-retest/dwi/sub-01_ses-retest_dwi.nii.gz
        /sub-01/ses-retest/func/sub-01_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-01/ses-retest/func/sub-01_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-01/ses-retest/func/sub-01_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-01/ses-retest/func/sub-01_ses-retest_task-linebisection_bold.nii.gz
        /sub-01/ses-retest/func/sub-01_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-01/ses-test/func/sub-01_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-01/ses-test/dwi/sub-01_ses-test_dwi.nii.gz
        /sub-01/ses-test/func/sub-01_ses-test_task-linebisection_bold.nii.gz
        /sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-01/ses-test/func/sub-01_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-01/ses-test/func/sub-01_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-02/ses-retest/dwi/sub-02_ses-retest_dwi.nii.gz
        /sub-02/ses-retest/func/sub-02_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-02/ses-retest/func/sub-02_ses-retest_task-linebisection_bold.nii.gz
        /sub-02/ses-retest/func/sub-02_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-02/ses-retest/func/sub-02_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-02/ses-retest/func/sub-02_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-02/ses-test/dwi/sub-02_ses-test_dwi.nii.gz
        /sub-02/ses-test/func/sub-02_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-02/ses-test/func/sub-02_ses-test_task-linebisection_bold.nii.gz
        /sub-02/ses-test/func/sub-02_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-02/ses-test/func/sub-02_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-02/ses-test/func/sub-02_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-03/ses-retest/dwi/sub-03_ses-retest_dwi.nii.gz
        /sub-03/ses-retest/func/sub-03_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz
        /sub-03/ses-retest/func/sub-03_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-03/ses-retest/func/sub-03_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-03/ses-retest/func/sub-03_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-03/ses-test/func/sub-03_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-03/ses-test/dwi/sub-03_ses-test_dwi.nii.gz
        /sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz
        /sub-03/ses-test/func/sub-03_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-03/ses-test/func/sub-03_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-03/ses-test/func/sub-03_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-04/ses-retest/func/sub-04_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-04/ses-retest/dwi/sub-04_ses-retest_dwi.nii.gz
        /sub-04/ses-retest/func/sub-04_ses-retest_task-linebisection_bold.nii.gz
        /sub-04/ses-retest/func/sub-04_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-04/ses-retest/func/sub-04_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-04/ses-retest/func/sub-04_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-04/ses-test/dwi/sub-04_ses-test_dwi.nii.gz
        /sub-04/ses-test/func/sub-04_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-04/ses-test/func/sub-04_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-04/ses-test/func/sub-04_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-04/ses-test/func/sub-04_ses-test_task-linebisection_bold.nii.gz
        /sub-04/ses-test/func/sub-04_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-05/ses-retest/dwi/sub-05_ses-retest_dwi.nii.gz
        /sub-05/ses-retest/func/sub-05_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-05/ses-retest/func/sub-05_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-05/ses-retest/func/sub-05_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-05/ses-retest/func/sub-05_ses-retest_task-linebisection_bold.nii.gz
        /sub-05/ses-retest/func/sub-05_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-05/ses-test/dwi/sub-05_ses-test_dwi.nii.gz
        /sub-05/ses-test/func/sub-05_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-05/ses-test/func/sub-05_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-05/ses-test/func/sub-05_ses-test_task-linebisection_bold.nii.gz
        /sub-05/ses-test/func/sub-05_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-05/ses-test/func/sub-05_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-06/ses-retest/func/sub-06_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-06/ses-retest/dwi/sub-06_ses-retest_dwi.nii.gz
        /sub-06/ses-retest/func/sub-06_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-06/ses-retest/func/sub-06_ses-retest_task-linebisection_bold.nii.gz
        /sub-06/ses-retest/func/sub-06_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-06/ses-retest/func/sub-06_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-06/ses-test/dwi/sub-06_ses-test_dwi.nii.gz
        /sub-06/ses-test/func/sub-06_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-06/ses-test/func/sub-06_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-06/ses-test/func/sub-06_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-06/ses-test/func/sub-06_ses-test_task-linebisection_bold.nii.gz
        /sub-06/ses-test/func/sub-06_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-07/ses-retest/dwi/sub-07_ses-retest_dwi.nii.gz
        /sub-07/ses-retest/func/sub-07_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-07/ses-retest/func/sub-07_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-07/ses-retest/func/sub-07_ses-retest_task-linebisection_bold.nii.gz
        /sub-07/ses-retest/func/sub-07_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-07/ses-retest/func/sub-07_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-07/ses-test/dwi/sub-07_ses-test_dwi.nii.gz
        /sub-07/ses-test/func/sub-07_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-07/ses-test/func/sub-07_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-07/ses-test/func/sub-07_ses-test_task-linebisection_bold.nii.gz
        /sub-07/ses-test/func/sub-07_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-07/ses-test/func/sub-07_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-08/ses-retest/dwi/sub-08_ses-retest_dwi.nii.gz
        /sub-08/ses-retest/func/sub-08_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-08/ses-retest/func/sub-08_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-08/ses-retest/func/sub-08_ses-retest_task-linebisection_bold.nii.gz
        /sub-08/ses-retest/func/sub-08_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-08/ses-retest/func/sub-08_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-08/ses-test/dwi/sub-08_ses-test_dwi.nii.gz
        /sub-08/ses-test/func/sub-08_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-08/ses-test/func/sub-08_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-08/ses-test/func/sub-08_ses-test_task-linebisection_bold.nii.gz
        /sub-08/ses-test/func/sub-08_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-08/ses-test/func/sub-08_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-09/ses-retest/dwi/sub-09_ses-retest_dwi.nii.gz
        /sub-09/ses-retest/func/sub-09_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-09/ses-retest/func/sub-09_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-09/ses-retest/func/sub-09_ses-retest_task-linebisection_bold.nii.gz
        /sub-09/ses-retest/func/sub-09_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-09/ses-retest/func/sub-09_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-09/ses-test/dwi/sub-09_ses-test_dwi.nii.gz
        /sub-09/ses-test/func/sub-09_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-09/ses-test/func/sub-09_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-09/ses-test/func/sub-09_ses-test_task-linebisection_bold.nii.gz
        /sub-09/ses-test/func/sub-09_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-09/ses-test/func/sub-09_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-10/ses-retest/dwi/sub-10_ses-retest_dwi.nii.gz
        /sub-10/ses-retest/func/sub-10_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-10/ses-retest/func/sub-10_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-10/ses-retest/func/sub-10_ses-retest_task-linebisection_bold.nii.gz
        /sub-10/ses-retest/func/sub-10_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-10/ses-retest/func/sub-10_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-10/ses-test/func/sub-10_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-10/ses-test/dwi/sub-10_ses-test_dwi.nii.gz
        /sub-10/ses-test/func/sub-10_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-10/ses-test/func/sub-10_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-10/ses-test/func/sub-10_ses-test_task-linebisection_bold.nii.gz
        /sub-10/ses-test/func/sub-10_ses-test_task-overtwordrepetition_bold.nii.gz

    4: You should should define 'TotalReadoutTime' for this file. If you don't provide this information field map correction using TOPUP might not be possible. (code: 9)
        /sub-01/ses-retest/dwi/sub-01_ses-retest_dwi.nii.gz
        /sub-01/ses-test/dwi/sub-01_ses-test_dwi.nii.gz
        /sub-02/ses-retest/dwi/sub-02_ses-retest_dwi.nii.gz
        /sub-02/ses-test/dwi/sub-02_ses-test_dwi.nii.gz
        /sub-03/ses-retest/dwi/sub-03_ses-retest_dwi.nii.gz
        /sub-03/ses-test/dwi/sub-03_ses-test_dwi.nii.gz
        /sub-04/ses-retest/dwi/sub-04_ses-retest_dwi.nii.gz
        /sub-04/ses-test/dwi/sub-04_ses-test_dwi.nii.gz
        /sub-05/ses-retest/dwi/sub-05_ses-retest_dwi.nii.gz
        /sub-05/ses-test/dwi/sub-05_ses-test_dwi.nii.gz
        /sub-06/ses-retest/dwi/sub-06_ses-retest_dwi.nii.gz
        /sub-06/ses-test/dwi/sub-06_ses-test_dwi.nii.gz
        /sub-07/ses-retest/dwi/sub-07_ses-retest_dwi.nii.gz
        /sub-07/ses-test/dwi/sub-07_ses-test_dwi.nii.gz
        /sub-08/ses-retest/dwi/sub-08_ses-retest_dwi.nii.gz
        /sub-08/ses-test/dwi/sub-08_ses-test_dwi.nii.gz
        /sub-09/ses-retest/dwi/sub-09_ses-retest_dwi.nii.gz
        /sub-09/ses-test/dwi/sub-09_ses-test_dwi.nii.gz
        /sub-10/ses-retest/dwi/sub-10_ses-retest_dwi.nii.gz
        /sub-10/ses-test/dwi/sub-10_ses-test_dwi.nii.gz

    5: You should should define 'SliceEncodingDirection' for this file. If you don't provide this information slice time correction will not be possible. (code: 14)
        /sub-01/ses-retest/func/sub-01_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-01/ses-retest/func/sub-01_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-01/ses-retest/func/sub-01_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-01/ses-retest/func/sub-01_ses-retest_task-linebisection_bold.nii.gz
        /sub-01/ses-retest/func/sub-01_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-01/ses-test/func/sub-01_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-01/ses-test/func/sub-01_ses-test_task-linebisection_bold.nii.gz
        /sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-01/ses-test/func/sub-01_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-01/ses-test/func/sub-01_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-02/ses-retest/func/sub-02_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-02/ses-retest/func/sub-02_ses-retest_task-linebisection_bold.nii.gz
        /sub-02/ses-retest/func/sub-02_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-02/ses-retest/func/sub-02_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-02/ses-retest/func/sub-02_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-02/ses-test/func/sub-02_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-02/ses-test/func/sub-02_ses-test_task-linebisection_bold.nii.gz
        /sub-02/ses-test/func/sub-02_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-02/ses-test/func/sub-02_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-02/ses-test/func/sub-02_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-03/ses-retest/func/sub-03_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-03/ses-retest/func/sub-03_ses-retest_task-linebisection_bold.nii.gz
        /sub-03/ses-retest/func/sub-03_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-03/ses-retest/func/sub-03_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-03/ses-retest/func/sub-03_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-03/ses-test/func/sub-03_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-03/ses-test/func/sub-03_ses-test_task-linebisection_bold.nii.gz
        /sub-03/ses-test/func/sub-03_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-03/ses-test/func/sub-03_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-03/ses-test/func/sub-03_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-04/ses-retest/func/sub-04_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-04/ses-retest/func/sub-04_ses-retest_task-linebisection_bold.nii.gz
        /sub-04/ses-retest/func/sub-04_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-04/ses-retest/func/sub-04_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-04/ses-retest/func/sub-04_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-04/ses-test/func/sub-04_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-04/ses-test/func/sub-04_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-04/ses-test/func/sub-04_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-04/ses-test/func/sub-04_ses-test_task-linebisection_bold.nii.gz
        /sub-04/ses-test/func/sub-04_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-05/ses-retest/func/sub-05_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-05/ses-retest/func/sub-05_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-05/ses-retest/func/sub-05_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-05/ses-retest/func/sub-05_ses-retest_task-linebisection_bold.nii.gz
        /sub-05/ses-retest/func/sub-05_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-05/ses-test/func/sub-05_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-05/ses-test/func/sub-05_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-05/ses-test/func/sub-05_ses-test_task-linebisection_bold.nii.gz
        /sub-05/ses-test/func/sub-05_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-05/ses-test/func/sub-05_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-06/ses-retest/func/sub-06_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-06/ses-retest/func/sub-06_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-06/ses-retest/func/sub-06_ses-retest_task-linebisection_bold.nii.gz
        /sub-06/ses-retest/func/sub-06_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-06/ses-retest/func/sub-06_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-06/ses-test/func/sub-06_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-06/ses-test/func/sub-06_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-06/ses-test/func/sub-06_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-06/ses-test/func/sub-06_ses-test_task-linebisection_bold.nii.gz
        /sub-06/ses-test/func/sub-06_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-07/ses-retest/func/sub-07_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-07/ses-retest/func/sub-07_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-07/ses-retest/func/sub-07_ses-retest_task-linebisection_bold.nii.gz
        /sub-07/ses-retest/func/sub-07_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-07/ses-retest/func/sub-07_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-07/ses-test/func/sub-07_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-07/ses-test/func/sub-07_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-07/ses-test/func/sub-07_ses-test_task-linebisection_bold.nii.gz
        /sub-07/ses-test/func/sub-07_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-07/ses-test/func/sub-07_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-08/ses-retest/func/sub-08_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-08/ses-retest/func/sub-08_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-08/ses-retest/func/sub-08_ses-retest_task-linebisection_bold.nii.gz
        /sub-08/ses-retest/func/sub-08_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-08/ses-retest/func/sub-08_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-08/ses-test/func/sub-08_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-08/ses-test/func/sub-08_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-08/ses-test/func/sub-08_ses-test_task-linebisection_bold.nii.gz
        /sub-08/ses-test/func/sub-08_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-08/ses-test/func/sub-08_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-09/ses-retest/func/sub-09_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-09/ses-retest/func/sub-09_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-09/ses-retest/func/sub-09_ses-retest_task-linebisection_bold.nii.gz
        /sub-09/ses-retest/func/sub-09_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-09/ses-retest/func/sub-09_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-09/ses-test/func/sub-09_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-09/ses-test/func/sub-09_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-09/ses-test/func/sub-09_ses-test_task-linebisection_bold.nii.gz
        /sub-09/ses-test/func/sub-09_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-09/ses-test/func/sub-09_ses-test_task-overtwordrepetition_bold.nii.gz
        /sub-10/ses-retest/func/sub-10_ses-retest_task-covertverbgeneration_bold.nii.gz
        /sub-10/ses-retest/func/sub-10_ses-retest_task-fingerfootlips_bold.nii.gz
        /sub-10/ses-retest/func/sub-10_ses-retest_task-linebisection_bold.nii.gz
        /sub-10/ses-retest/func/sub-10_ses-retest_task-overtverbgeneration_bold.nii.gz
        /sub-10/ses-retest/func/sub-10_ses-retest_task-overtwordrepetition_bold.nii.gz
        /sub-10/ses-test/func/sub-10_ses-test_task-covertverbgeneration_bold.nii.gz
        /sub-10/ses-test/func/sub-10_ses-test_task-fingerfootlips_bold.nii.gz
        /sub-10/ses-test/func/sub-10_ses-test_task-overtverbgeneration_bold.nii.gz
        /sub-10/ses-test/func/sub-10_ses-test_task-linebisection_bold.nii.gz
        /sub-10/ses-test/func/sub-10_ses-test_task-overtwordrepetition_bold.nii.gz

As you can see I tested node 4.2 and 5.3. The problematic lines are those where orange:bids-validator filo$ bin/bids-validator ../BIDS-examples/ds114 does not produce any output.

from bids-validator.

constellates commented on July 19, 2024

I'm still unable to reproduce this. I re-cloned the repos and ran through a few versions of node without issue.

A few differences or things to try

I'm managing node versions through NVM I'll try using brew in case they are potentially using different builds.
What version of OSX are you using? I can also test in ubuntu to see if anything is different there.
It's often a good idea to remove and re-install node modules when changing versions. I doubt this is it; I've been able to switch versions just now without reinstalling, but it's worth a try.
I'll continue trying to reproduce this, but also added a new branch (https://github.com/INCF/bids-validator/tree/issue-70) with logging in that section of code to see where it is failing for you and what is working properly. If you can, try it and send the logs.

from bids-validator.

chrisgorgo commented on July 19, 2024

I have removed and reinstalled both global and local npm modules to no avail. Your branch is giving me this output:

orange:bids-validator filo$ bin/bids-validator ../BIDS-examples/ds114
1 { name: 'sub-01_ses-retest_T1w.nii.gz',
  path: '../BIDS-examples/ds114/sub-01/ses-retest/anat/sub-01_ses-retest_T1w.nii.gz',
  relativePath: '/sub-01/ses-retest/anat/sub-01_ses-retest_T1w.nii.gz' }
1 { name: 'sub-01_ses-retest_dwi.nii.gz',
  path: '../BIDS-examples/ds114/sub-01/ses-retest/dwi/sub-01_ses-retest_dwi.nii.gz',
  relativePath: '/sub-01/ses-retest/dwi/sub-01_ses-retest_dwi.nii.gz' }
1 { name: 'sub-01_ses-retest_task-covertverbgeneration_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-01/ses-retest/func/sub-01_ses-retest_task-covertverbgeneration_bold.nii.gz',
  relativePath: '/sub-01/ses-retest/func/sub-01_ses-retest_task-covertverbgeneration_bold.nii.gz' }
1 { name: 'sub-01_ses-retest_task-fingerfootlips_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-01/ses-retest/func/sub-01_ses-retest_task-fingerfootlips_bold.nii.gz',
  relativePath: '/sub-01/ses-retest/func/sub-01_ses-retest_task-fingerfootlips_bold.nii.gz' }
1 { name: 'sub-01_ses-retest_task-linebisection_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-01/ses-retest/func/sub-01_ses-retest_task-linebisection_bold.nii.gz',
  relativePath: '/sub-01/ses-retest/func/sub-01_ses-retest_task-linebisection_bold.nii.gz' }
1 { name: 'sub-01_ses-retest_task-overtverbgeneration_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-01/ses-retest/func/sub-01_ses-retest_task-overtverbgeneration_bold.nii.gz',
  relativePath: '/sub-01/ses-retest/func/sub-01_ses-retest_task-overtverbgeneration_bold.nii.gz' }
1 { name: 'sub-01_ses-retest_task-overtwordrepetition_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-01/ses-retest/func/sub-01_ses-retest_task-overtwordrepetition_bold.nii.gz',
  relativePath: '/sub-01/ses-retest/func/sub-01_ses-retest_task-overtwordrepetition_bold.nii.gz' }
1 { name: 'sub-01_ses-test_T1w.nii.gz',
  path: '../BIDS-examples/ds114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz',
  relativePath: '/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz' }
1 { name: 'sub-01_ses-test_dwi.nii.gz',
  path: '../BIDS-examples/ds114/sub-01/ses-test/dwi/sub-01_ses-test_dwi.nii.gz',
  relativePath: '/sub-01/ses-test/dwi/sub-01_ses-test_dwi.nii.gz' }
1 { name: 'sub-01_ses-test_task-covertverbgeneration_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-01/ses-test/func/sub-01_ses-test_task-covertverbgeneration_bold.nii.gz',
  relativePath: '/sub-01/ses-test/func/sub-01_ses-test_task-covertverbgeneration_bold.nii.gz' }
1 { name: 'sub-01_ses-test_task-fingerfootlips_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz',
  relativePath: '/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz' }
1 { name: 'sub-01_ses-test_task-linebisection_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-01/ses-test/func/sub-01_ses-test_task-linebisection_bold.nii.gz',
  relativePath: '/sub-01/ses-test/func/sub-01_ses-test_task-linebisection_bold.nii.gz' }
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1 { name: 'sub-06_ses-test_task-overtwordrepetition_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-06/ses-test/func/sub-06_ses-test_task-overtwordrepetition_bold.nii.gz',
  relativePath: '/sub-06/ses-test/func/sub-06_ses-test_task-overtwordrepetition_bold.nii.gz' }
1 { name: 'sub-07_ses-retest_T1w.nii.gz',
  path: '../BIDS-examples/ds114/sub-07/ses-retest/anat/sub-07_ses-retest_T1w.nii.gz',
  relativePath: '/sub-07/ses-retest/anat/sub-07_ses-retest_T1w.nii.gz' }
1 { name: 'sub-07_ses-retest_dwi.nii.gz',
  path: '../BIDS-examples/ds114/sub-07/ses-retest/dwi/sub-07_ses-retest_dwi.nii.gz',
  relativePath: '/sub-07/ses-retest/dwi/sub-07_ses-retest_dwi.nii.gz' }
1 { name: 'sub-07_ses-retest_task-covertverbgeneration_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-07/ses-retest/func/sub-07_ses-retest_task-covertverbgeneration_bold.nii.gz',
  relativePath: '/sub-07/ses-retest/func/sub-07_ses-retest_task-covertverbgeneration_bold.nii.gz' }
1 { name: 'sub-07_ses-retest_task-fingerfootlips_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-07/ses-retest/func/sub-07_ses-retest_task-fingerfootlips_bold.nii.gz',
  relativePath: '/sub-07/ses-retest/func/sub-07_ses-retest_task-fingerfootlips_bold.nii.gz' }
1 { name: 'sub-07_ses-retest_task-linebisection_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-07/ses-retest/func/sub-07_ses-retest_task-linebisection_bold.nii.gz',
  relativePath: '/sub-07/ses-retest/func/sub-07_ses-retest_task-linebisection_bold.nii.gz' }
1 { name: 'sub-07_ses-retest_task-overtverbgeneration_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-07/ses-retest/func/sub-07_ses-retest_task-overtverbgeneration_bold.nii.gz',
  relativePath: '/sub-07/ses-retest/func/sub-07_ses-retest_task-overtverbgeneration_bold.nii.gz' }
1 { name: 'sub-07_ses-retest_task-overtwordrepetition_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-07/ses-retest/func/sub-07_ses-retest_task-overtwordrepetition_bold.nii.gz',
  relativePath: '/sub-07/ses-retest/func/sub-07_ses-retest_task-overtwordrepetition_bold.nii.gz' }
1 { name: 'sub-07_ses-test_T1w.nii.gz',
  path: '../BIDS-examples/ds114/sub-07/ses-test/anat/sub-07_ses-test_T1w.nii.gz',
  relativePath: '/sub-07/ses-test/anat/sub-07_ses-test_T1w.nii.gz' }
1 { name: 'sub-07_ses-test_dwi.nii.gz',
  path: '../BIDS-examples/ds114/sub-07/ses-test/dwi/sub-07_ses-test_dwi.nii.gz',
  relativePath: '/sub-07/ses-test/dwi/sub-07_ses-test_dwi.nii.gz' }
1 { name: 'sub-07_ses-test_task-covertverbgeneration_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-07/ses-test/func/sub-07_ses-test_task-covertverbgeneration_bold.nii.gz',
  relativePath: '/sub-07/ses-test/func/sub-07_ses-test_task-covertverbgeneration_bold.nii.gz' }
1 { name: 'sub-07_ses-test_task-fingerfootlips_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-07/ses-test/func/sub-07_ses-test_task-fingerfootlips_bold.nii.gz',
  relativePath: '/sub-07/ses-test/func/sub-07_ses-test_task-fingerfootlips_bold.nii.gz' }
1 { name: 'sub-07_ses-test_task-linebisection_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-07/ses-test/func/sub-07_ses-test_task-linebisection_bold.nii.gz',
  relativePath: '/sub-07/ses-test/func/sub-07_ses-test_task-linebisection_bold.nii.gz' }
1 { name: 'sub-07_ses-test_task-overtverbgeneration_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-07/ses-test/func/sub-07_ses-test_task-overtverbgeneration_bold.nii.gz',
  relativePath: '/sub-07/ses-test/func/sub-07_ses-test_task-overtverbgeneration_bold.nii.gz' }
1 { name: 'sub-07_ses-test_task-overtwordrepetition_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-07/ses-test/func/sub-07_ses-test_task-overtwordrepetition_bold.nii.gz',
  relativePath: '/sub-07/ses-test/func/sub-07_ses-test_task-overtwordrepetition_bold.nii.gz' }
1 { name: 'sub-08_ses-retest_T1w.nii.gz',
  path: '../BIDS-examples/ds114/sub-08/ses-retest/anat/sub-08_ses-retest_T1w.nii.gz',
  relativePath: '/sub-08/ses-retest/anat/sub-08_ses-retest_T1w.nii.gz' }
1 { name: 'sub-08_ses-retest_dwi.nii.gz',
  path: '../BIDS-examples/ds114/sub-08/ses-retest/dwi/sub-08_ses-retest_dwi.nii.gz',
  relativePath: '/sub-08/ses-retest/dwi/sub-08_ses-retest_dwi.nii.gz' }
1 { name: 'sub-08_ses-retest_task-covertverbgeneration_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-08/ses-retest/func/sub-08_ses-retest_task-covertverbgeneration_bold.nii.gz',
  relativePath: '/sub-08/ses-retest/func/sub-08_ses-retest_task-covertverbgeneration_bold.nii.gz' }
1 { name: 'sub-08_ses-retest_task-fingerfootlips_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-08/ses-retest/func/sub-08_ses-retest_task-fingerfootlips_bold.nii.gz',
  relativePath: '/sub-08/ses-retest/func/sub-08_ses-retest_task-fingerfootlips_bold.nii.gz' }
1 { name: 'sub-08_ses-retest_task-linebisection_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-08/ses-retest/func/sub-08_ses-retest_task-linebisection_bold.nii.gz',
  relativePath: '/sub-08/ses-retest/func/sub-08_ses-retest_task-linebisection_bold.nii.gz' }
1 { name: 'sub-08_ses-retest_task-overtverbgeneration_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-08/ses-retest/func/sub-08_ses-retest_task-overtverbgeneration_bold.nii.gz',
  relativePath: '/sub-08/ses-retest/func/sub-08_ses-retest_task-overtverbgeneration_bold.nii.gz' }
1 { name: 'sub-08_ses-retest_task-overtwordrepetition_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-08/ses-retest/func/sub-08_ses-retest_task-overtwordrepetition_bold.nii.gz',
  relativePath: '/sub-08/ses-retest/func/sub-08_ses-retest_task-overtwordrepetition_bold.nii.gz' }
1 { name: 'sub-08_ses-test_T1w.nii.gz',
  path: '../BIDS-examples/ds114/sub-08/ses-test/anat/sub-08_ses-test_T1w.nii.gz',
  relativePath: '/sub-08/ses-test/anat/sub-08_ses-test_T1w.nii.gz' }
1 { name: 'sub-08_ses-test_dwi.nii.gz',
  path: '../BIDS-examples/ds114/sub-08/ses-test/dwi/sub-08_ses-test_dwi.nii.gz',
  relativePath: '/sub-08/ses-test/dwi/sub-08_ses-test_dwi.nii.gz' }
1 { name: 'sub-08_ses-test_task-covertverbgeneration_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-08/ses-test/func/sub-08_ses-test_task-covertverbgeneration_bold.nii.gz',
  relativePath: '/sub-08/ses-test/func/sub-08_ses-test_task-covertverbgeneration_bold.nii.gz' }
1 { name: 'sub-08_ses-test_task-fingerfootlips_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-08/ses-test/func/sub-08_ses-test_task-fingerfootlips_bold.nii.gz',
  relativePath: '/sub-08/ses-test/func/sub-08_ses-test_task-fingerfootlips_bold.nii.gz' }
1 { name: 'sub-08_ses-test_task-linebisection_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-08/ses-test/func/sub-08_ses-test_task-linebisection_bold.nii.gz',
  relativePath: '/sub-08/ses-test/func/sub-08_ses-test_task-linebisection_bold.nii.gz' }
1 { name: 'sub-08_ses-test_task-overtverbgeneration_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-08/ses-test/func/sub-08_ses-test_task-overtverbgeneration_bold.nii.gz',
  relativePath: '/sub-08/ses-test/func/sub-08_ses-test_task-overtverbgeneration_bold.nii.gz' }
1 { name: 'sub-08_ses-test_task-overtwordrepetition_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-08/ses-test/func/sub-08_ses-test_task-overtwordrepetition_bold.nii.gz',
  relativePath: '/sub-08/ses-test/func/sub-08_ses-test_task-overtwordrepetition_bold.nii.gz' }
1 { name: 'sub-09_ses-retest_T1w.nii.gz',
  path: '../BIDS-examples/ds114/sub-09/ses-retest/anat/sub-09_ses-retest_T1w.nii.gz',
  relativePath: '/sub-09/ses-retest/anat/sub-09_ses-retest_T1w.nii.gz' }
1 { name: 'sub-09_ses-retest_dwi.nii.gz',
  path: '../BIDS-examples/ds114/sub-09/ses-retest/dwi/sub-09_ses-retest_dwi.nii.gz',
  relativePath: '/sub-09/ses-retest/dwi/sub-09_ses-retest_dwi.nii.gz' }
1 { name: 'sub-09_ses-retest_task-covertverbgeneration_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-09/ses-retest/func/sub-09_ses-retest_task-covertverbgeneration_bold.nii.gz',
  relativePath: '/sub-09/ses-retest/func/sub-09_ses-retest_task-covertverbgeneration_bold.nii.gz' }
1 { name: 'sub-09_ses-retest_task-fingerfootlips_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-09/ses-retest/func/sub-09_ses-retest_task-fingerfootlips_bold.nii.gz',
  relativePath: '/sub-09/ses-retest/func/sub-09_ses-retest_task-fingerfootlips_bold.nii.gz' }
1 { name: 'sub-09_ses-retest_task-linebisection_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-09/ses-retest/func/sub-09_ses-retest_task-linebisection_bold.nii.gz',
  relativePath: '/sub-09/ses-retest/func/sub-09_ses-retest_task-linebisection_bold.nii.gz' }
1 { name: 'sub-09_ses-retest_task-overtverbgeneration_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-09/ses-retest/func/sub-09_ses-retest_task-overtverbgeneration_bold.nii.gz',
  relativePath: '/sub-09/ses-retest/func/sub-09_ses-retest_task-overtverbgeneration_bold.nii.gz' }
1 { name: 'sub-09_ses-retest_task-overtwordrepetition_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-09/ses-retest/func/sub-09_ses-retest_task-overtwordrepetition_bold.nii.gz',
  relativePath: '/sub-09/ses-retest/func/sub-09_ses-retest_task-overtwordrepetition_bold.nii.gz' }
1 { name: 'sub-09_ses-test_T1w.nii.gz',
  path: '../BIDS-examples/ds114/sub-09/ses-test/anat/sub-09_ses-test_T1w.nii.gz',
  relativePath: '/sub-09/ses-test/anat/sub-09_ses-test_T1w.nii.gz' }
1 { name: 'sub-09_ses-test_dwi.nii.gz',
  path: '../BIDS-examples/ds114/sub-09/ses-test/dwi/sub-09_ses-test_dwi.nii.gz',
  relativePath: '/sub-09/ses-test/dwi/sub-09_ses-test_dwi.nii.gz' }
1 { name: 'sub-09_ses-test_task-covertverbgeneration_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-09/ses-test/func/sub-09_ses-test_task-covertverbgeneration_bold.nii.gz',
  relativePath: '/sub-09/ses-test/func/sub-09_ses-test_task-covertverbgeneration_bold.nii.gz' }
1 { name: 'sub-09_ses-test_task-fingerfootlips_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-09/ses-test/func/sub-09_ses-test_task-fingerfootlips_bold.nii.gz',
  relativePath: '/sub-09/ses-test/func/sub-09_ses-test_task-fingerfootlips_bold.nii.gz' }
1 { name: 'sub-09_ses-test_task-linebisection_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-09/ses-test/func/sub-09_ses-test_task-linebisection_bold.nii.gz',
  relativePath: '/sub-09/ses-test/func/sub-09_ses-test_task-linebisection_bold.nii.gz' }
1 { name: 'sub-09_ses-test_task-overtverbgeneration_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-09/ses-test/func/sub-09_ses-test_task-overtverbgeneration_bold.nii.gz',
  relativePath: '/sub-09/ses-test/func/sub-09_ses-test_task-overtverbgeneration_bold.nii.gz' }
1 { name: 'sub-09_ses-test_task-overtwordrepetition_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-09/ses-test/func/sub-09_ses-test_task-overtwordrepetition_bold.nii.gz',
  relativePath: '/sub-09/ses-test/func/sub-09_ses-test_task-overtwordrepetition_bold.nii.gz' }
1 { name: 'sub-10_ses-retest_T1w.nii.gz',
  path: '../BIDS-examples/ds114/sub-10/ses-retest/anat/sub-10_ses-retest_T1w.nii.gz',
  relativePath: '/sub-10/ses-retest/anat/sub-10_ses-retest_T1w.nii.gz' }
1 { name: 'sub-10_ses-retest_dwi.nii.gz',
  path: '../BIDS-examples/ds114/sub-10/ses-retest/dwi/sub-10_ses-retest_dwi.nii.gz',
  relativePath: '/sub-10/ses-retest/dwi/sub-10_ses-retest_dwi.nii.gz' }
1 { name: 'sub-10_ses-retest_task-covertverbgeneration_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-10/ses-retest/func/sub-10_ses-retest_task-covertverbgeneration_bold.nii.gz',
  relativePath: '/sub-10/ses-retest/func/sub-10_ses-retest_task-covertverbgeneration_bold.nii.gz' }
1 { name: 'sub-10_ses-retest_task-fingerfootlips_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-10/ses-retest/func/sub-10_ses-retest_task-fingerfootlips_bold.nii.gz',
  relativePath: '/sub-10/ses-retest/func/sub-10_ses-retest_task-fingerfootlips_bold.nii.gz' }
1 { name: 'sub-10_ses-retest_task-linebisection_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-10/ses-retest/func/sub-10_ses-retest_task-linebisection_bold.nii.gz',
  relativePath: '/sub-10/ses-retest/func/sub-10_ses-retest_task-linebisection_bold.nii.gz' }
1 { name: 'sub-10_ses-retest_task-overtverbgeneration_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-10/ses-retest/func/sub-10_ses-retest_task-overtverbgeneration_bold.nii.gz',
  relativePath: '/sub-10/ses-retest/func/sub-10_ses-retest_task-overtverbgeneration_bold.nii.gz' }
1 { name: 'sub-10_ses-retest_task-overtwordrepetition_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-10/ses-retest/func/sub-10_ses-retest_task-overtwordrepetition_bold.nii.gz',
  relativePath: '/sub-10/ses-retest/func/sub-10_ses-retest_task-overtwordrepetition_bold.nii.gz' }
1 { name: 'sub-10_ses-test_T1w.nii.gz',
  path: '../BIDS-examples/ds114/sub-10/ses-test/anat/sub-10_ses-test_T1w.nii.gz',
  relativePath: '/sub-10/ses-test/anat/sub-10_ses-test_T1w.nii.gz' }
1 { name: 'sub-10_ses-test_dwi.nii.gz',
  path: '../BIDS-examples/ds114/sub-10/ses-test/dwi/sub-10_ses-test_dwi.nii.gz',
  relativePath: '/sub-10/ses-test/dwi/sub-10_ses-test_dwi.nii.gz' }
1 { name: 'sub-10_ses-test_task-covertverbgeneration_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-10/ses-test/func/sub-10_ses-test_task-covertverbgeneration_bold.nii.gz',
  relativePath: '/sub-10/ses-test/func/sub-10_ses-test_task-covertverbgeneration_bold.nii.gz' }
1 { name: 'sub-10_ses-test_task-fingerfootlips_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-10/ses-test/func/sub-10_ses-test_task-fingerfootlips_bold.nii.gz',
  relativePath: '/sub-10/ses-test/func/sub-10_ses-test_task-fingerfootlips_bold.nii.gz' }
1 { name: 'sub-10_ses-test_task-linebisection_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-10/ses-test/func/sub-10_ses-test_task-linebisection_bold.nii.gz',
  relativePath: '/sub-10/ses-test/func/sub-10_ses-test_task-linebisection_bold.nii.gz' }
1 { name: 'sub-10_ses-test_task-overtverbgeneration_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-10/ses-test/func/sub-10_ses-test_task-overtverbgeneration_bold.nii.gz',
  relativePath: '/sub-10/ses-test/func/sub-10_ses-test_task-overtverbgeneration_bold.nii.gz' }
1 { name: 'sub-10_ses-test_task-overtwordrepetition_bold.nii.gz',
  path: '../BIDS-examples/ds114/sub-10/ses-test/func/sub-10_ses-test_task-overtwordrepetition_bold.nii.gz',
  relativePath: '/sub-10/ses-test/func/sub-10_ses-test_task-overtwordrepetition_bold.nii.gz' }

BTW @wtriplett is also seeing this bug.

from bids-validator.

wtriplett commented on July 19, 2024

Hi yes — I have seen this and will try to provide a reproduction case later today.

Best,
Bill

BTW @wtriplett is also seeing this bug.

—
Reply to this email directly or view it on GitHub.

from bids-validator.

constellates commented on July 19, 2024

This is strange. The node fs readstream isn't doing anything for you. We can re-write the partial file reading with another method, only the decompression has to be done through a stream, but it would be good to know why this isn't working in some cases. I can mock this issue by commenting out the fs.createReadStream section but then the test suite fails for me due to a time out and so does circle CI so this definitely seems environment specific. Does the test suite time out for you on master? I'll try adding an alternative file reading strategy to the issue-70 branch and let you know when it's available.

from bids-validator.

chrisgorgo commented on July 19, 2024

I think this bug affects the stack used on CircleCI because the tests are
passing even though they should not (@wtripplet added a feature checking
for double tab characters in .tsv files which should raise errors in our
example datasets that included double tabs like this one
https://github.com/INCF/BIDS-examples/blob/master/7t_trt/sub-09/sub-09_sessions.tsv
).

On Fri, Jan 8, 2016 at 11:54 AM, constellates [email protected]
wrote:

This is strange. The node fs readstream isn't doing anything for you. We
can re-write the partial file reading with another method, only the
decompression has to be done through a stream, but it would be good to know
why this isn't working in some cases. I can mock this issue by commenting
out the fs.createReadStream section but then the test suite fails for me
due to a time out and so does circle CI so this definitely seems
environment specific. Does the test suite time out for you on master? I'll
try adding an alternative file reading strategy to the issue-70 branch and
let you know when it's available.

—
Reply to this email directly or view it on GitHub
https://github.com/INCF/bids-validator/issues/70#issuecomment-170106552.

from bids-validator.

constellates commented on July 19, 2024

Are they passing locally as well? We do have one test that runs a dataset with files with real headers. That's what's timing out if I try to mock this issue.

I've also updated the issue-70 branch with a different file reading strategy and left some logging in case this doesn't work for you.

If it fails as well I'm wondering if it's related to this section where fs gets conditionally imported (https://github.com/INCF/bids-validator/blob/master/utils/files.js#L10). If it's still failing on the issue-70 branch you might try commenting out lines 10, 13, 14 and 15.

from bids-validator.

chrisgorgo commented on July 19, 2024

Yes the tests pass on master locally (but they shouldn't, because of the bug in example data I mentioned above).

I have updated the issue-70 branch and I'm getting the following output (error):

orange:bids-validator filo$ bin/bids-validator ../BIDS-examples/ds114
status: null
fd: 18
status: null
fd: 20
status: null
fd: 21
status: null
fd: 19
status: null
fd: 22
status: null
fd: 23
status: null
fd: 24
status: null
fd: 26
status: null
fd: 25
status: null
fd: 27
status: null
fd: 29
status: null
fd: 30
status: null
fd: 28
status: null
fd: 31
status: null
fd: 32
status: null
fd: 33
status: null
fd: 35
status: null
fd: 34
status: null
fd: 36
status: null
fd: 37
status: null
fd: 39
status: null
fd: 40
status: null
fd: 38
status: null
fd: 41
status: null
fd: 42
status: null
fd: 43
status: null
fd: 44
status: null
fd: 46
status: null
fd: 45
status: null
fd: 48
status: null
fd: 47
status: null
fd: 49
status: null
fd: 50
status: null
fd: 52
status: null
fd: 51
status: null
fd: 53
status: null
fd: 54
status: null
fd: 56
status: null
fd: 55
status: null
fd: 57
status: null
fd: 59
status: null
fd: 60
status: null
fd: 58
status: null
fd: 61
status: null
fd: 63
status: null
fd: 64
status: null
fd: 62
status: null
fd: 66
status: null
fd: 65
status: null
fd: 67
status: null
fd: 68
status: null
fd: 69
status: null
fd: 70
status: null
fd: 72
status: null
fd: 71
status: null
fd: 73
status: null
fd: 74
status: null
fd: 75
status: null
fd: 76
status: null
fd: 77
status: null
fd: 78
status: null
fd: 79
status: null
fd: 80
status: null
fd: 81
status: null
fd: 82
status: null
fd: 84
status: null
fd: 83
status: null
fd: 85
status: null
fd: 87
status: null
fd: 86
status: null
fd: 88
status: null
fd: 89
status: null
fd: 90
status: null
fd: 91
status: null
fd: 92
status: null
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/Users/filo/drive/workspace/bids-validator/validators/nii.js:51
                header.dim[4]                                                    // header 4th dimension
                          ^

TypeError: Cannot read property '4' of undefined
    at NIFTI (/Users/filo/drive/workspace/bids-validator/validators/nii.js:51:27)
    at /Users/filo/drive/workspace/bids-validator/validators/bids.js:172:25
    at Gunzip.<anonymous> (/Users/filo/drive/workspace/bids-validator/utils/files.js:122:17)
    at emitOne (events.js:77:13)
    at Gunzip.emit (events.js:169:7)
    at Zlib._handle.onerror (zlib.js:366:10)

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constellates commented on July 19, 2024

Is this a dataset with empty niftis? It's showing it's trying to read 500 bytes and is reading 0 bytes of each file. If I point to an empty nifti test dataset locally I can now reproduce this issue identically. We have a work around implemented ('ignoreNiftiHeaders') for testing and using the CLI with empty scans. If this is the issue, I'll add an error to catch this if the ignore option is not being used.

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chrisgorgo commented on July 19, 2024

I think in general errors when reading NIFTI files should be reported in a nicer way (for example when people try using the validator on invalid files).

Otherwise I think your branch fixes the issue. I tested it on empty and full datasets with node4 and node5. It also turns out the the "n/a" checking feature throws a warning instead of an error and that's why the tests pass. I'll fix that in a future PR.

from bids-validator.

constellates commented on July 19, 2024

Do you have something in mind for improving on file reading error message? Or what might be missing from them currently, aside from specific cases like this that were missed?

Here's the two errors we currently have for file reading related issues.

26: {
    severity: 'error',
    reason:   "We were unable to read the contents of this file."
},
...
28: {
    severity: 'error',
    reason: "This file ends in the .gz extension but is not actually gzipped."
},

I was planning to add this one

{
    severity: 'error',
    reason: "This file is too small to contain the minimum NIfTI header."
}

but if we need a different strategy for file reading error handling I can hold off.

Edit: I can also add one for invalid NifTIs.

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chrisgorgo commented on July 19, 2024

I think this would be sufficient. Thanks!

On Fri, Jan 8, 2016 at 2:18 PM, constellates [email protected]
wrote:

Do you have something in mind for improving on file reading error message?
Or what might be missing from them currently, aside from specific cases
like this that were missed?

Here's the two errors we currently have for file reading related issues.

26: {
severity: 'error',
reason: "We were unable to read the contents of this file."
},
...
28: {
severity: 'error',
reason: "This file ends in the .gz extension but is not actually gzipped."
},

I was planning to add this one

{
severity: 'error',
reason: "This file is too small to contain the minimum NIfTI header."
}

but if we need a different strategy for file reading error handling I can
hold off.

—
Reply to this email directly or view it on GitHub
https://github.com/INCF/bids-validator/issues/70#issuecomment-170143373.

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command line client silently fails to read .nii.gz files about bids-validator HOT 13 CLOSED

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