error: file not available

[jcohenadad]

I am missing some files when running datalad get, see example for sub01-ses001:

julien-macbook:~/temp/neuromod $ datalad install -r git@github.com:courtois-neuromod/anat.git
[INFO   ] scanning for annexed files (this may take some time)                                                       
[INFO   ] Unable to parse git config from origin                                                                     
[INFO   ] [ERROR] [Errno 32] Broken pipe (BrokenPipeError) 
[INFO   ] Remote origin does not have git-annex installed; setting annex-ignore
|   This could be a problem with the git-annex installation on the remote. Please make sure that git-annex-shell is available in PATH when you ssh into the remote. Once you have fixed the git-annex installation, run: git annex enableremote origin 
[INFO   ] RIA store unavailable. -caused by- file:///data/neuromod/ria-sequoia/data/neuromod/ria-sequoia/ria-layout-version not found. -caused by- [Errno 2] No such file or directory: '/data/neuromod/ria-sequoia/ria-layout-version' 
[INFO   ] access to 2 dataset siblings ria-beluga-storage, cneuromod.anat.mri.sensitive not auto-enabled, enable with:
|       datalad siblings -d "/Users/julien/temp/neuromod/anat" enable -s SIBLING 
install(ok): /Users/julien/temp/neuromod/anat (dataset)
[INFO   ] Installing Dataset(/Users/julien/temp/neuromod/anat) to get /Users/julien/temp/neuromod/anat recursively 
julien-macbook:~/temp/neuromod $ cd anat/      
julien-macbook:~/temp/neuromod/anat $ datalad get sub-01/ses-001/
get(ok): sub-01/ses-001/anat/sub-01_ses-001_T1w.nii.gz (file) [from cneuromod.anat.mri...]                                                                                                 
get(ok): sub-01/ses-001/anat/sub-01_ses-001_T2w.nii.gz (file) [from cneuromod.anat.mri...]                                                                                                 
get(ok): sub-01/ses-001/anat/sub-01_ses-001_UNIT1.nii.gz (file) [from cneuromod.anat.mri...]
get(error): sub-01/ses-001/anat/sub-01_ses-001_acq-axial_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_acq-coronal_bp-cspine_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_acq-coronal_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_acq-sagittal_bp-cspine_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_acq-sagittal_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_bp-cspine_T2starw.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_bp-cspine_T2w.nii.gz (file) [from cneuromod.anat.mri...]
get(error): sub-01/ses-001/anat/sub-01_ses-001_bp-cspine_flip-1_mt-off_MTS.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_bp-cspine_flip-1_mt-on_MTS.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_bp-cspine_flip-2_mt-off_MTS.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_flip-1_mt-off_MTS.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_flip-1_mt-on_MTS.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_flip-2_mt-off_MTS.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_inv-1_MP2RAGE.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_inv-2_MP2RAGE.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_rec-dis2d_UNIT1.nii.gz (file) [from cneuromod.anat.mri...]
get(error): sub-01/ses-001/anat/sub-01_ses-001_rec-dis2d_flip-1_mt-off_MTS.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_rec-dis2d_flip-1_mt-on_MTS.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_rec-dis2d_flip-2_mt-off_MTS.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_rec-dis2d_inv-1_MP2RAGE.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_rec-dis2d_inv-2_MP2RAGE.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_rec-norm_T1w.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_rec-norm_T2w.nii.gz (file) [from cneuromod.anat.mri...]
get(error): sub-01/ses-001/anat/sub-01_ses-001_rec-norm_mod-T1w_defacemask.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(ok): sub-01/ses-001/dwi/sub-01_ses-001_dir-AP_bp-cspine_dwi.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/dwi/sub-01_ses-001_dir-AP_dwi.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/dwi/sub-01_ses-001_dir-AP_sbref.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/dwi/sub-01_ses-001_dir-PA_dwi.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/dwi/sub-01_ses-001_dir-PA_sbref.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/fmap/sub-01_ses-001_acq-anat_TB1TFL.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/fmap/sub-01_ses-001_acq-famp_TB1TFL.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_epi.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_epi.nii.gz (file) [from cneuromod.anat.mri...]
get(error): sub-01/ses-001/sub-01_ses-001_scans.tsv (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(impossible): sub-01/ses-001 (directory) [could not get some content in /Users/julien/temp/neuromod/anat/sub-01/ses-001 ['/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_acq-axial_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_acq-coronal_bp-cspine_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_acq-coronal_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_acq-sagittal_bp-cspine_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_acq-sagittal_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_bp-cspine_flip-1_mt-off_MTS.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_bp-cspine_flip-1_mt-on_MTS.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_bp-cspine_flip-2_mt-off_MTS.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_flip-1_mt-off_MTS.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_flip-1_mt-on_MTS.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_flip-2_mt-off_MTS.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_rec-dis2d_flip-1_mt-off_MTS.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_rec-dis2d_flip-1_mt-on_MTS.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_rec-dis2d_flip-2_mt-off_MTS.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_rec-norm_mod-T1w_defacemask.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/sub-01_ses-001_scans.tsv']]
action summary:
  get (error: 16, impossible: 1, ok: 21)

[jcohenadad]

Is it possible this issue is related to the change in file names?

[bpinsard]

This is due to some files being flagged as sensitive (non-defaced or sensitive info): mainly the localizer series and the _scans.tsv (containing the real datetime of acquisition). I see how it is disturbing having these errors when downloading files. I will investigate if git-annex allows a default filter when getting files to exclude these. Another option would be to deface the localizer and change the datetime to fake dates (still keeping the same intervals for longitudinal analysis requiring it) which is something we already planned for the functional data. If not, we might need to remove these from the release (still keeping them in the datalad history).

[bpinsard]

However the defacemask should be downloadable. Will look into it.

[jcohenadad]

This is due to some files being flagged as sensitive (non-defaced or sensitive info): mainly the localizer series and the _scans.tsv (containing the real datetime of acquisition). I see how it is disturbing having these errors when downloading files.

maybe this explanation is valid for some files (eg localizer), but this file for example does not show the face (axial acquisition in the neck):

get(error): sub-01/ses-001/anat/sub-01_ses-001_bp-cspine_flip-1_mt-on_MTS.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]

[bpinsard]

The defacing was skipped on that images, which is a mistake. And this image still needs defacing as the FoV covers a good chunk of the teeth which are identifiable features (I have no knowledge about forensic odontology but it's better to be on the safe side). Will fix it ASAP.

[bpinsard]

This should be fixed, you can datalad update --merge and check that you are on tag 0.10.1 . Now only the localizers and _scans.tsv should be inaccessible.

[jcohenadad]

julien-macbook:~/temp/neuromod/anat $ datalad update --merge
[INFO   ] Fetching updates for Dataset(/Users/julien/temp/neuromod/anat) 
                                                                                                                                                                        merge(ok): . (dataset) [Merged origin/main]                                                                                                                               
update.annex_merge(ok): . (dataset) [Merged annex branch]
update(ok): . (dataset)
action summary:
  merge (ok: 1)
  update (ok: 1)
  update.annex_merge (ok: 1)
julien-macbook:~/temp/neuromod/anat $ git tag
0.10.0
0.10.1
2020-alpha2
julien-macbook:~/temp/neuromod/anat $ datalad get sub-01/ses-001/
get(error): sub-01/ses-001/anat/sub-01_ses-001_acq-axial_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]            
get(error): sub-01/ses-001/anat/sub-01_ses-001_acq-coronal_bp-cspine_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_acq-coronal_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_acq-sagittal_bp-cspine_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_acq-sagittal_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_bp-cspine_flip-1_mt-off_MTS.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_bp-cspine_flip-1_mt-on_MTS.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_bp-cspine_flip-2_mt-off_MTS.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_flip-1_mt-off_MTS.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_flip-1_mt-on_MTS.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_flip-2_mt-off_MTS.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_rec-dis2d_flip-1_mt-off_MTS.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_rec-dis2d_flip-1_mt-on_MTS.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_rec-dis2d_flip-2_mt-off_MTS.nii.gz (file) [from cneuromod.anat.mri...]
get(error): sub-01/ses-001/anat/sub-01_ses-001_rec-norm_mod-T1w_defacemask.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/sub-01_ses-001_scans.tsv (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(impossible): sub-01/ses-001 (directory) [could not get some content in /Users/julien/temp/neuromod/anat/sub-01/ses-001 ['/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_acq-axial_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_acq-coronal_bp-cspine_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_acq-coronal_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_acq-sagittal_bp-cspine_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_acq-sagittal_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_rec-norm_mod-T1w_defacemask.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/sub-01_ses-001_scans.tsv']]
action summary:
  get (error: 7, impossible: 1, ok: 9)

looks good! thank you! 🙏

[jcohenadad]

Reopening because looking at another session, some scans that should be there are not there:

get(error): sub-01/ses-002/anat/sub-01_ses-002_bp-cspine_T2w.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-002/anat/sub-01_ses-002_inv-1_MP2RAGE.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-002/anat/sub-01_ses-002_inv-2_MP2RAGE.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-002/anat/sub-01_ses-002_rec-dis2d_UNIT1.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-002/anat/sub-01_ses-002_rec-dis2d_inv-1_MP2RAGE.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-002/anat/sub-01_ses-002_rec-dis2d_inv-2_MP2RAGE.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]

Terminal output

```console julien-macbook:~/temp/neuromod/anat $ datalad get sub-01/ses-002/ get(ok): sub-01/ses-002/anat/sub-01_ses-002_T1w.nii.gz (file) [from cneuromod.anat.mri...] get(ok): sub-01/ses-002/anat/sub-01_ses-002_T2w.nii.gz (file) [from cneuromod.anat.mri...] get(error): sub-01/ses-002/anat/sub-01_ses-002_UNIT1.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)] get(error): sub-01/ses-002/anat/sub-01_ses-002_acq-axial_bp-cspine_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)] get(error): sub-01/ses-002/anat/sub-01_ses-002_acq-axial_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)] get(error): sub-01/ses-002/anat/sub-01_ses-002_acq-axial_rec-dis2d_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)] get(error): sub-01/ses-002/anat/sub-01_ses-002_acq-coronal_bp-cspine_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)] get(error): sub-01/ses-002/anat/sub-01_ses-002_acq-coronal_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)] get(error): sub-01/ses-002/anat/sub-01_ses-002_acq-coronal_rec-dis2d_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)] get(error): sub-01/ses-002/anat/sub-01_ses-002_acq-sagittal_bp-cspine_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)] get(error): sub-01/ses-002/anat/sub-01_ses-002_acq-sagittal_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)] get(error): sub-01/ses-002/anat/sub-01_ses-002_acq-sagittal_rec-dis2d_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)] get(ok): sub-01/ses-002/anat/sub-01_ses-002_bp-cspine_T2starw.nii.gz (file) [from cneuromod.anat.mri...] get(error): sub-01/ses-002/anat/sub-01_ses-002_bp-cspine_T2w.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)] get(ok): sub-01/ses-002/anat/sub-01_ses-002_bp-cspine_flip-1_mt-off_MTS.nii.gz (file) [from cneuromod.anat.mri...] get(ok): sub-01/ses-002/anat/sub-01_ses-002_bp-cspine_flip-1_mt-on_MTS.nii.gz (file) [from cneuromod.anat.mri...] get(ok): sub-01/ses-002/anat/sub-01_ses-002_bp-cspine_flip-2_mt-off_MTS.nii.gz (file) [from cneuromod.anat.mri...] get(ok): sub-01/ses-002/anat/sub-01_ses-002_flip-1_mt-off_MTS.nii.gz (file) [from cneuromod.anat.mri...] get(ok): sub-01/ses-002/anat/sub-01_ses-002_flip-1_mt-on_MTS.nii.gz (file) [from cneuromod.anat.mri...] get(ok): sub-01/ses-002/anat/sub-01_ses-002_flip-2_mt-off_MTS.nii.gz (file) [from cneuromod.anat.mri...] get(error): sub-01/ses-002/anat/sub-01_ses-002_inv-1_MP2RAGE.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)] get(error): sub-01/ses-002/anat/sub-01_ses-002_inv-2_MP2RAGE.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)] get(error): sub-01/ses-002/anat/sub-01_ses-002_rec-dis2d_UNIT1.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)] get(ok): sub-01/ses-002/anat/sub-01_ses-002_rec-dis2d_flip-1_mt-off_MTS.nii.gz (file) [from cneuromod.anat.mri...] get(ok): sub-01/ses-002/anat/sub-01_ses-002_rec-dis2d_flip-1_mt-on_MTS.nii.gz (file) [from cneuromod.anat.mri...] get(ok): sub-01/ses-002/anat/sub-01_ses-002_rec-dis2d_flip-2_mt-off_MTS.nii.gz (file) [from cneuromod.anat.mri...] get(error): sub-01/ses-002/anat/sub-01_ses-002_rec-dis2d_inv-1_MP2RAGE.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)] get(error): sub-01/ses-002/anat/sub-01_ses-002_rec-dis2d_inv-2_MP2RAGE.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)] get(ok): sub-01/ses-002/anat/sub-01_ses-002_rec-norm_T1w.nii.gz (file) [from cneuromod.anat.mri...] get(ok): sub-01/ses-002/anat/sub-01_ses-002_rec-norm_T2w.nii.gz (file) [from cneuromod.anat.mri...] get(error): sub-01/ses-002/anat/sub-01_ses-002_rec-norm_mod-T1w_defacemask.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)] get(ok): sub-01/ses-002/dwi/sub-01_ses-002_dir-AP_bp-cspine_dwi.nii.gz (file) [from cneuromod.anat.mri...] get(ok): sub-01/ses-002/dwi/sub-01_ses-002_dir-AP_dwi.nii.gz (file) [from cneuromod.anat.mri...] get(ok): sub-01/ses-002/dwi/sub-01_ses-002_dir-AP_sbref.nii.gz (file) [from cneuromod.anat.mri...] get(ok): sub-01/ses-002/dwi/sub-01_ses-002_dir-PA_dwi.nii.gz (file) [from cneuromod.anat.mri...] get(ok): sub-01/ses-002/dwi/sub-01_ses-002_dir-PA_sbref.nii.gz (file) [from cneuromod.anat.mri...] get(ok): sub-01/ses-002/fmap/sub-01_ses-002_acq-anat_TB1TFL.nii.gz (file) [from cneuromod.anat.mri...] get(ok): sub-01/ses-002/fmap/sub-01_ses-002_acq-famp_TB1TFL.nii.gz (file) [from cneuromod.anat.mri...] get(ok): sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_epi.nii.gz (file) [from cneuromod.anat.mri...] get(ok): sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_epi.nii.gz (file) [from cneuromod.anat.mri...] get(error): sub-01/ses-002/sub-01_ses-002_scans.tsv (file) [not available; (Note that these git remotes have annex-ignore set: origin)] get(ok): sub-01/ses-002/swi/sub-01_ses-002_minIP.nii.gz (file) [from cneuromod.anat.mri...] get(ok): sub-01/ses-002/swi/sub-01_ses-002_swi.nii.gz (file) [from cneuromod.anat.mri...] get(impossible): sub-01/ses-002 (directory) [could not get some content in /Users/julien/temp/neuromod/anat/sub-01/ses-002 ['/Users/julien/temp/neuromod/anat/sub-01/ses-002/anat/sub-01_ses-002_UNIT1.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-002/anat/sub-01_ses-002_acq-axial_bp-cspine_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-002/anat/sub-01_ses-002_acq-axial_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-002/anat/sub-01_ses-002_acq-axial_rec-dis2d_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-002/anat/sub-01_ses-002_acq-coronal_bp-cspine_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-002/anat/sub-01_ses-002_acq-coronal_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-002/anat/sub-01_ses-002_acq-coronal_rec-dis2d_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-002/anat/sub-01_ses-002_acq-sagittal_bp-cspine_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-002/anat/sub-01_ses-002_acq-sagittal_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-002/anat/sub-01_ses-002_acq-sagittal_rec-dis2d_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-002/anat/sub-01_ses-002_bp-cspine_T2w.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-002/anat/sub-01_ses-002_inv-1_MP2RAGE.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-002/anat/sub-01_ses-002_inv-2_MP2RAGE.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-002/anat/sub-01_ses-002_rec-dis2d_UNIT1.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-002/anat/sub-01_ses-002_rec-dis2d_inv-1_MP2RAGE.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-002/anat/sub-01_ses-002_rec-dis2d_inv-2_MP2RAGE.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-002/anat/sub-01_ses-002_rec-norm_mod-T1w_defacemask.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-002/sub-01_ses-002_scans.tsv']] action summary: get (error: 18, impossible: 1, ok: 25) ```

[jcohenadad]

Also: these JSON sidecar files are missing:

sub-01_ses-002_bp-cspine_flip-1_mt-off_MTS.json
sub-01_ses-002_bp-cspine_flip-1_mt-on_MTS.json
sub-01_ses-002_bp-cspine_flip-2_mt-off_MTS.json

(needed for computing MTsat and T1)

[bpinsard]

Oops, both should be fixed now. Thanks for all the troubleshooting

[jcohenadad]

LGTM! I'll reopen if I spot other issues. Thanks a bunch!

Tagging @mathieuboudreau so he can also try brain processing on his end

[jcohenadad]

fresh download (done on 2022-11-08), still getting some errors-- from user facing standpoint this is confusing. See: https://github.com/courtois-neuromod/cneuromod_docs/issues/83#issuecomment-1307913296

[jcohenadad]

tagging @bpinsard

[bpinsard]

Should be fixed, now verified by CI/CD testing.