Skip to content

Commit 31ef34d

Browse files
oestebanoesteban
authored
Merge pull request #38 from nipreps/talks/bootcamp-day1-02-patch
enh: continue working on BIDS' slides
2 parents 29cdf27 + c33092b commit 31ef34d

File tree

1 file changed

+139
-43
lines changed
  • docs/assets/fmriprep-bootcamp-geneva2024/day1-02-bids

1 file changed

+139
-43
lines changed

‎docs/assets/fmriprep-bootcamp-geneva2024/day1-02-bids/index.html

Lines changed: 139 additions & 43 deletions
Original file line numberDiff line numberDiff line change
@@ -462,40 +462,38 @@
462462
<i class="fa-solid fa-folder-open"></i> my_dataset/<br />
463463
.pad-left[<i class="fa-solid fa-file-lines"></i> CHANGES]<br />
464464
.pad-left[<i class="fa-solid fa-file-lines"></i> README]<br />
465-
.pad-left[<i class="fa-solid fa-circle-info"></i> dataset_description.json]<br />
466-
.pad-left[<i class="fa-solid fa-circle-info"></i> participants.json]<br />
465+
.pad-left[<i class="fa-solid fa-paperclip"></i> dataset_description.json]<br />
466+
.pad-left[<i class="fa-solid fa-paperclip"></i> participants.json]<br />
467467
.pad-left[<i class="fa-solid fa-table"></i> participants.tsv]<br />
468-
.pad-left[<i class="fa-solid fa-circle-info"></i> scans.json]<br />
468+
.pad-left[<i class="fa-solid fa-paperclip"></i> scans.json]<br />
469469
.pad-left[<i class="fa-solid fa-folder-open"></i> sub-11]<br />
470470
.pad-left[.pad-left[<i class="fa-solid fa-folder-open"></i> anat/]]<br />
471-
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-circle-info"></i> sub-11_T2w.json]]]<br />
471+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_T2w.json]]]<br />
472472
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_T2w.nii.gz]]]<br />
473-
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-circle-info"></i> sub-11_acq-denoised_T1w.json]]]<br />
473+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_acq-denoised_T1w.json]]]<br />
474474
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_acq-denoised_T1w.nii.gz]]]<br />
475-
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-circle-info"></i> sub-11_acq-mp2rage_T1w.json]]]<br />
475+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_acq-mp2rage_T1w.json]]]<br />
476476
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_acq-mp2rage_T1w.nii.gz]]]<br />
477477
.pad-left[.pad-left[<i class="fa-solid fa-folder-open"></i> fmap/]]<br />
478-
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-circle-info"></i> sub-11_magnitude1.json]]]<br />
478+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_magnitude1.json]]]<br />
479479
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_magnitude1.nii.gz]]]<br />
480-
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-circle-info"></i> sub-11_magnitude2.json]]]<br />
480+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_magnitude2.json]]]<br />
481481
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_magnitude2.nii.gz]]]<br />
482-
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-circle-info"></i> sub-11_phasediff.json]]]<br />
482+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_phasediff.json]]]<br />
483483
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_phasediff.nii.gz]]]<br />
484484
.pad-left[.pad-left[<i class="fa-solid fa-folder-open"></i> func/]]<br />
485-
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-circle-info"></i> sub-11_task-mixed_bold.json]]]<br />
485+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_task-mixed_bold.json]]]<br />
486486
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_task-mixed_bold.nii.gz]]]<br />
487487
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-table"></i> sub-11_task-mixed_events.tsv]]]<br />
488-
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-circle-info"></i> sub-11_task-rest_bold.json]]]<br />
488+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_task-rest_bold.json]]]<br />
489489
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_task-rest_bold.nii.gz]]]<br />
490490
.pad-left[.pad-left[<i class="fa-solid fa-table"></i> sub-11_scans.tsv]]<br />
491491
.pad-left[<i class="fa-solid fa-folder"></i> sub-14]<br />
492492
.pad-left[<i class="fa-solid fa-folder"></i> sub-15]<br />
493493
]
494494
]
495+
.right-column2.larger[
495496

496-
---
497-
498-
.right-column2[
499497
* BIDS is a directory structure, based on common practices
500498

501499
* Builds on existing standards (NIfTI, JSON, TSV)
@@ -511,49 +509,147 @@
511509

512510
---
513511

514-
.right-column2[
515-
* Basic metadata in the file names
516-
512+
.right-column2[.no-bullet[* .larger[Basic metadata in the file names]
517513
* Subject, session, imaging modality, etc.
518-
* Generally just enough to assign unique names
519-
]
520-
514+
* Generally just enough to assign unique names]]
521515
--
522-
.right-column2[
523-
* NIfTI headers and JSON sidecars contain detailed,
524-
image-related metadata
525-
]
516+
.right-column2[.no-bullet[* .larger[NIfTI headers and *JSON sidecars* contain detailed,
517+
image-related metadata]]]
526518
--
527-
.right-column2[
528-
* [`dataset_description.json`](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#dataset_descriptionjson),
529-
[`participants.tsv`](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#participants-file),
530-
[`sessions.tsv`](https://bids-specification.readthedocs.io/en/stable/05-longitudinal-and-multi-site-studies.html#sessions-file),
531-
and [`scans.tsv`](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#scans-file)
532-
record study-level metadata that may not be associated
533-
with specific images
534-
]
519+
.right-column2[.no-bullet[* .larger[Study-level metadata]
520+
* Not necessarily associated with specific files
521+
* [`dataset_description.json`](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#dataset_descriptionjson),
522+
[`participants.tsv`](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#participants-file),
523+
[`sessions.tsv`](https://bids-specification.readthedocs.io/en/stable/05-longitudinal-and-multi-site-studies.html#sessions-file),
524+
and [`scans.tsv`](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#scans-file)
525+
]]
535526

536527
---
528+
name: newsection
537529
layout: true
538-
template: newsection
539530

531+
.perma-sidebar[
532+
<p class="rotate">
533+
<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0; height: 20px; padding-top: 6px;" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a>
534+
<span style="padding-left: 10px; font-weight: 600;">Day 1 :: Brain Imaging Data Structure</span>
535+
</p>
536+
]
540537
---
541538

542-
# Bidsification
543-
544-
Constructing a BIDS dataset can be tedious and error-prone, so there are several
545-
[converters](https://bids.neuroimaging.io/benefits.html#converters).
539+
# Converting from DICOM into BIDS
546540

547-
<figure style="width: 50%">
548-
![:img DICOM to BIDS conversion, 100%](images/dicom-reorganization-transparent-black_1000x477.png)
549-
</figure>
541+
.left-column-mid.small[
542+
.pad-left[
543+
<i class="fa-solid fa-folder-open"></i> my_dataset/<br />
544+
.pad-left[<i class="fa-solid fa-folder-open"></i> sub-11]<br />
545+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 10 - anat-T1w_acq-mp2rage_run-01_UNI_Images.dicom]]<br />
546+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 11 - anat-T1w_acq-mp2rage_run-01_UNI-DEN.dicom]]<br />
547+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 12 - anat-T1w_acq-mp2rage_run-01_INV2.dicom]]<br />
548+
.pad-left[.pad-left[<i class="fa-solid fa-folder-open"></i> 16 - fmap-gre_acq-siemens_run-01/]]<br />
549+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 1.3.12.2.1107.5.2.61.237203.20[...]25.MR.dcm]]]<br />
550+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 1.3.12.2.1107.5.2.61.237203.20[..]33.MR.dcm]]]<br />
551+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 17 - fmap-gre_acq-siemens_run-01.dicom ]]<br />
552+
.pad-left[.pad-left[<i class="fa-solid fa-folder-open"></i> 18 - func-bold_acq-midRes_task-rest_run-01/ ]]<br />
553+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 1.3.12.2.1107.5.2.61.237203.20[...]25.MR.dcm]]]<br />
554+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-ellipsis"></i>]]]<br />
555+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 1.3.12.2.1107.5.2.61.237203.20[..]33.MR.dcm]]]<br />
556+
.pad-left[.pad-left[<i class="fa-solid fa-folder-open"></i> 20 - func-bold_acq-midRes_task-mixed_run-01/ ]]<br />
557+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 1.3.12.2.1107.5.2.61.237203.20[...]25.MR.dcm]]]<br />
558+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-ellipsis"></i>]]]<br />
559+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 1.3.12.2.1107.5.2.61.237203.20[..]33.MR.dcm]]]<br />
560+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 22 - anat-T2w_acq-p6_run-01.dicom]]<br />
561+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 7 - anat-T1w_acq-mp2rage_run-01_INV1.dicom]]<br />
562+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 8 - anat-T1w_acq-mp2rage_run-01_T1_Images.dicom]]<br />
563+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 9 - anat-T1w_acq-mp2rage_run-01_T1_Images.dicom]]<br />
564+
.pad-left[<i class="fa-solid fa-folder"></i> sub-14]<br />
565+
.pad-left[<i class="fa-solid fa-folder"></i> sub-15]<br />
566+
]
567+
]
550568

551-
DICOM images store their relevant metadata internally, but naming conventions tend
552-
to be scanner/institution-specific.
569+
.right-column-mid[
570+
.no-bullet[
571+
* .larger[DICOM (Digital Imaging and Communications in Medicine)]
572+
* was originally meant for storage and transmission within/between machines.
573+
* .larger[DICOM structures store their relevant metadata internally,]
574+
* but structure and fields tend to be vendor- & institution-specific.
553575

554-
The [Heuristic DICOM Converter](https://heudiconv.readthedocs.io/) (HeuDiConv) and
576+
* .larger[Constructing a BIDS dataset can be tedious and error-prone, so there are several
577+
[converters](https://bids.neuroimaging.io/benefits.html#converters).]
578+
* The [Heuristic DICOM Converter](https://heudiconv.readthedocs.io/) (HeuDiConv) and
555579
[BIDSCoin](https://bidscoin.readthedocs.io/en/stable/) allow you to specify the mapping and
556580
apply in bulk. Both build off of [dcm2niix](https://github.com/rordenlab/dcm2niix/).
581+
]
582+
]
583+
584+
---
585+
586+
# Converting from DICOM into BIDS
587+
588+
.left-column-mid.small[
589+
.pad-left[
590+
<i class="fa-solid fa-folder-open"></i> my_dataset/<br />
591+
.pad-left[<i class="fa-solid fa-folder-open"></i> sub-11]<br />
592+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 10 - anat-T1w_acq-mp2rage_run-01_UNI_Images.dicom]]<br />
593+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 11 - anat-T1w_acq-mp2rage_run-01_UNI-DEN.dicom]]<br />
594+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 12 - anat-T1w_acq-mp2rage_run-01_INV2.dicom]]<br />
595+
.pad-left[.pad-left[<i class="fa-solid fa-folder-open"></i> 16 - fmap-gre_acq-siemens_run-01/]]<br />
596+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 1.3.12.2.1107.5.2.61.237203.20[...]25.MR.dcm]]]<br />
597+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 1.3.12.2.1107.5.2.61.237203.20[..]33.MR.dcm]]]<br />
598+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 17 - fmap-gre_acq-siemens_run-01.dicom ]]<br />
599+
.pad-left[.pad-left[<i class="fa-solid fa-folder-open"></i> 18 - func-bold_acq-midRes_task-rest_run-01/ ]]<br />
600+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 1.3.12.2.1107.5.2.61.237203.20[...]25.MR.dcm]]]<br />
601+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-ellipsis"></i>]]]<br />
602+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 1.3.12.2.1107.5.2.61.237203.20[..]33.MR.dcm]]]<br />
603+
.pad-left[.pad-left[<i class="fa-solid fa-folder-open"></i> 20 - func-bold_acq-midRes_task-mixed_run-01/ ]]<br />
604+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 1.3.12.2.1107.5.2.61.237203.20[...]25.MR.dcm]]]<br />
605+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-ellipsis"></i>]]]<br />
606+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 1.3.12.2.1107.5.2.61.237203.20[..]33.MR.dcm]]]<br />
607+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 22 - anat-T2w_acq-p6_run-01.dicom]]<br />
608+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 7 - anat-T1w_acq-mp2rage_run-01_INV1.dicom]]<br />
609+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 8 - anat-T1w_acq-mp2rage_run-01_T1_Images.dicom]]<br />
610+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 9 - anat-T1w_acq-mp2rage_run-01_T1_Images.dicom]]<br />
611+
.pad-left[<i class="fa-solid fa-folder"></i> sub-14]<br />
612+
.pad-left[<i class="fa-solid fa-folder"></i> sub-15]<br />
613+
]
614+
]
615+
616+
.right-column-mid.small[
617+
.pad-left[
618+
<i class="fa-solid fa-folder-open"></i> my_dataset/<br />
619+
.pad-left[<i class="fa-solid fa-file-lines"></i> CHANGES]<br />
620+
.pad-left[<i class="fa-solid fa-file-lines"></i> README]<br />
621+
.pad-left[<i class="fa-solid fa-paperclip"></i> dataset_description.json]<br />
622+
.pad-left[<i class="fa-solid fa-paperclip"></i> participants.json]<br />
623+
.pad-left[<i class="fa-solid fa-table"></i> participants.tsv]<br />
624+
.pad-left[<i class="fa-solid fa-paperclip"></i> scans.json]<br />
625+
.pad-left[<i class="fa-solid fa-folder-open"></i> sub-11]<br />
626+
.pad-left[.pad-left[<i class="fa-solid fa-folder-open"></i> anat/]]<br />
627+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_T2w.json]]]<br />
628+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_T2w.nii.gz]]]<br />
629+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_acq-denoised_T1w.json]]]<br />
630+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_acq-denoised_T1w.nii.gz]]]<br />
631+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_acq-mp2rage_T1w.json]]]<br />
632+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_acq-mp2rage_T1w.nii.gz]]]<br />
633+
.pad-left[.pad-left[<i class="fa-solid fa-folder-open"></i> fmap/]]<br />
634+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_magnitude1.json]]]<br />
635+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_magnitude1.nii.gz]]]<br />
636+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_magnitude2.json]]]<br />
637+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_magnitude2.nii.gz]]]<br />
638+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_phasediff.json]]]<br />
639+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_phasediff.nii.gz]]]<br />
640+
.pad-left[.pad-left[<i class="fa-solid fa-folder-open"></i> func/]]<br />
641+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_task-mixed_bold.json]]]<br />
642+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_task-mixed_bold.nii.gz]]]<br />
643+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-table"></i> sub-11_task-mixed_events.tsv]]]<br />
644+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_task-rest_bold.json]]]<br />
645+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_task-rest_bold.nii.gz]]]<br />
646+
.pad-left[.pad-left[<i class="fa-solid fa-table"></i> sub-11_scans.tsv]]<br />
647+
.pad-left[<i class="fa-solid fa-folder"></i> sub-14]<br />
648+
.pad-left[<i class="fa-solid fa-folder"></i> sub-15]<br />
649+
]
650+
]
651+
652+
<i class="fa-solid fa-circle-right" style="margin-top: 20%; font-size: 1.7em"></i>
557653

558654
---
559655

0 commit comments

Comments
 (0)