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cpp-lln-lab / bidspm

an SPM centric BIDS app
https://bidspm.readthedocs.io/en/latest/general_information.html
GNU General Public License v3.0
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What BIDS name do we want for our derivatives ? #417

Closed Remi-Gau closed 2 years ago

Remi-Gau commented 3 years ago

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

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

Remi-Gau commented 3 years ago

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

Remi-Gau commented 2 years ago

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

Without the workflow names segmentationSkullstripping

With the workflow names out