What BIDS name do we want for our derivatives ? #417
Description
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
runand thesesentity - 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.nii | sub-01_task-auditory_desc-confounds_regressors.tsv |
| rp_asub-01_task-auditory_bold.nii | 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