What BIDS name do we want for our derivatives ?

[Remi-Gau]

As discussed starting a discussion thread on how files will be renamed into BIDS derivatives.

One thing to clarify: the final output of a preprocessing pipeline (for func or anat) MUST be described as desc-preproc. This is done to facilitate knowing which file to "grab" no matter what software is used afterwards.

Also "provenance tracking" knowing the "parent" files of given file can be done in BIDS derivatives in the side-car json files, so it might not have to be encoded in the filename.

@mohmdrezk @marcobarilari @CerenB #

TODO

• show examples of filenames with the run and the ses entity
• break down the renaming tables by "workflow" to show how files are renamed after each analysis step

func

SPM	BIDS
s6usub-01_task-auditory_bold.nii	sub-01_task-auditory_space-individual_desc-smth6_bold.nii
s6rsub-01_task-auditory_bold.nii	sub-01_task-auditory_space-individual_desc-smth6_bold.nii
s6uasub-01_task-auditory_bold.nii	sub-01_task-auditory_space-individual_desc-smth6_bold.nii
s6rasub-01_task-auditory_bold.nii	sub-01_task-auditory_space-individual_desc-smth6_bold.nii
s6wusub-01_task-auditory_bold.nii	sub-01_task-auditory_space-IXI549Space_desc-smth6_bold.nii
s6wrsub-01_task-auditory_bold.nii	sub-01_task-auditory_space-IXI549Space_desc-smth6_bold.nii
s6wuasub-01_task-auditory_bold.nii	sub-01_task-auditory_space-IXI549Space_desc-smth6_bold.nii
s6wrasub-01_task-auditory_bold.nii	sub-01_task-auditory_space-IXI549Space_desc-smth6_bold.nii
s6sub-01_task-auditory_bold.nii	sub-01_task-auditory_desc-smth6_bold.nii
rp_sub-01_task-auditory_bold.txt	sub-01_task-auditory_desc-confounds_regressors.tsv
rp_asub-01_task-auditory_bold.txt	sub-01_task-auditory_desc-confounds_regressors.tsv
usub-01_task-auditory_bold.nii	sub-01_task-auditory_space-individual_desc-preproc_bold.nii
uasub-01_task-auditory_bold.nii	sub-01_task-auditory_space-individual_desc-preproc_bold.nii
rsub-01_task-auditory_bold.nii	sub-01_task-auditory_space-individual_desc-preproc_bold.nii
rasub-01_task-auditory_bold.nii	sub-01_task-auditory_space-individual_desc-preproc_bold.nii
std_usub-01_task-auditory_bold.nii	sub-01_task-auditory_space-individual_desc-std_bold.nii
std_uasub-01_task-auditory_bold.nii	sub-01_task-auditory_space-individual_desc-std_bold.nii

anat

SPM	BIDS
wc1sub-01_T1w.nii	sub-01_space-IXI549Space_res-bold_label-GM_probseg.nii
wc2sub-01_T1w.nii	sub-01_space-IXI549Space_res-bold_label-WM_probseg.nii
wc3sub-01_T1w.nii	sub-01_space-IXI549Space_res-bold_label-CSF_probseg.nii
rc1sub-01_T1w.nii	sub-01_space-individual_res-bold_label-GM_probseg.nii
rc2sub-01_T1w.nii	sub-01_space-individual_res-bold_label-WM_probseg.nii
rc3sub-01_T1w.nii	sub-01_space-individual_res-bold_label-CSF_probseg.nii
wmsub-01_T1w.nii	sub-01_space-IXI549Space_res-r1pt0_T1w.nii
wmsub-01_desc-skullstripped_T1w.nii	sub-01_space-IXI549Space_res-r1pt0_desc-preproc_T1w.nii
msub-01_desc-skullstripped_T1w.nii	sub-01_space-individual_desc-preproc_T1w.nii
wsub-01_desc-skullstripped_T1w.nii	sub-01_space-individual_res-r1pt0_desc-preproc_T1w.nii
msub-01_space-individual_desc-something_label-brain_mask.nii	sub-01_space-individual_label-brain_mask.nii
c1sub-01_T1w.surf.gii	sub-01_desc-pialsurf_T1w.gii

Not listed: some of the outputs of the segmentation done by the ALI toolbox for lesion detection

[Remi-Gau]

Note: show examples of filenames with the run and the ses entity.

[Remi-Gau]

Possibly helpful, adding some DAGs (directed acyclic graphs for the different workflows)

Without the workflow names

With the workflow names

[marcobarilari]

These graphs are useful but at the same time hard to read so not sure if they can help in tracking the files before and after bids renaming.

[Remi-Gau]

I agree: they are too cluttered but in case someone wants to explore them

[marcobarilari]

So, don't know if still valid or too late but it looks good to me. I have played a lot with the dev branch of CPP_SPM and can say that the names are very clear and at least for my use case I am missing no name or any of them is creating confusion or problems.

[Remi-Gau]

Ideally I would like to add information in some json file explaining where each file came from because despite its non-bids character the spm prefix makes it very easy to know where the file came from (data provenance).