[ENH] Store BOLD reference images

[oesteban]

Changes proposed in this pull request

• Stores BOLD reference images in the output folder (following new RC1 conventions).
• Updates DerivativesDataSink not to insert the _<bids_type>_ in the middle of every derivative name.

Documentation that should be reviewed

[effigies]

Just want to say: I think the renaming process should be all-or-nothing. Once it starts, we should finish before releasing. Do we want to make a release before starting to merge PRs like this?

[oesteban]

Do we want to make a release before starting to merge PRs like this?

Yesss

[effigies]

I don't think this qualifies as a bold.nii.gz, as it's not a 4D time series. We didn't try to get a ref suffix (or perhaps boldref, since there is no longer a bold entry) into RC1, but we can still use it as long as there isn't a more appropriate suffix in the spec.

Pinging BIDS-meister @chrisfilo for a second opinion, though.

[chrisgorgo]

You're right - I would use a new suffix and be ready to change it some time in the future when this is standardized.

…

On Thu, Oct 4, 2018, 5:56 AM Chris Markiewicz ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In .circleci/ds005_outputs.txt <#1306 (comment)>: > -fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz -fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-MNI152NLin2009cAsym_preproc.nii.gz -fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-MNI152NLin2009cAsym_variant-smoothAROMAnonaggr_preproc.nii.gz -fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-T1w_brainmask.nii.gz -fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-T1w_label-aparcaseg_roi.nii.gz -fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-T1w_label-aseg_roi.nii.gz -fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-T1w_preproc.nii.gz +fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_AROMAnoiseICs.csv +fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_confounds.tsv +fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_MELODICmix.tsv +fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-cifti_variant-space1_preproc.dtseries.json +fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-cifti_variant-space1_preproc.dtseries.nii +fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5.L.func.gii +fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5.R.func.gii +fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_brainmask.nii.gz +fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-3dref_bold.nii.gz I don't think this qualifies as a bold.nii.gz, as it's not a 4D time series. We didn't try to get a ref suffix (or perhaps boldref, since there is no longer a bold entry) into RC1, but we can still use it as long as there isn't a more appropriate suffix in the spec. Pinging BIDS-meister @chrisfilo <https://github.com/chrisfilo> for a second opinion, though. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1306 (review)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAOkp487rz40_1t2nFZ5JMMaBOjm7D1cks5uhgVxgaJpZM4XHLmv> .

[oesteban]

thumbs up?

[effigies]

Sure. Let's move pretty quickly on the rest of the renamings, then. I listed the anat ones. I'll check for any functional ones that aren't covered by that in the morning.