Skip to content

Commit fa14d08

Browse files
oestebanoesteban
committed
enh: more about reproin, heudiconv
1 parent 31ef34d commit fa14d08

File tree

1 file changed

+189
-12
lines changed
  • docs/assets/fmriprep-bootcamp-geneva2024/day1-02-bids

1 file changed

+189
-12
lines changed

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

Lines changed: 189 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -492,6 +492,9 @@
492492
.pad-left[<i class="fa-solid fa-folder"></i> sub-15]<br />
493493
]
494494
]
495+
496+
---
497+
495498
.right-column2.larger[
496499

497500
* BIDS is a directory structure, based on common practices
@@ -525,15 +528,9 @@
525528
]]
526529

527530
---
528-
name: newsection
531+
template: newsection
529532
layout: true
530533

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-
]
537534
---
538535

539536
# Converting from DICOM into BIDS
@@ -653,16 +650,196 @@
653650

654651
---
655652

656-
# Bidsification: ReproIn
653+
# DICOM-to-BIDS: ReproIn
654+
655+
.center[[ReproIn](https://github.com/ReproNim/reproin) standardizes scanner conventions:]
657656

658-
The [ReproIn](https://github.com/ReproNim/reproin) project aims to
659-
standardize scanner conventions, to eliminate the need to rewrite these mappings.
657+
<figure style="width: 60%">
658+
![:img HCPh-sops-naming, 100%](https://www.axonlab.org/hcph-sops/assets/images/launch_sequence.jpg)
659+
<figcaption>From <a href="https://www.axonlab.org/hcph-sops">the HCPh SOPs</a>;
660+
doi:![:doi](10.6084/m9.figshare.19579873.v1)</figcaption>
661+
</figure>
662+
663+
---
660664

661-
<figure style="width: 40%">
665+
<figure style="width: 60%">
662666
![:img ReproIn conversion schema, 100%](images/dbic-conversions_cropped.png)
663667
<figcaption>From <a href="https://github.com/ReproNim/reproin/blob/master/README.md#overall-workflow">ReproIn</a>;
664668
doi:![:doi](10.5281/zenodo.1207117)</figcaption>
665-
</figure>
669+
670+
???
671+
672+
Please note that this figure is OUT OF DATE. For example, the anatomicals are called anat-T1W__, anat-T2w__ etc.
673+
674+
---
675+
676+
# DICOM-to-BIDS: HeuDiConv
677+
678+
.boxed-content.no-bullet[
679+
680+
* .large[<i class="fa-solid fa-circle-chevron-right"></i> **Heu**ristic **DI**COM** Conv**erter: maps DICOM metadata into BIDS]
681+
682+
* .large[<i class="fa-solid fa-circle-chevron-right"></i> Mappings are encoded within the *heuristic file*]
683+
684+
* The `.heudiconv/` folder contains the metadata that can be employed in the *heuristic file* to define mappings.<br /><br />
685+
686+
<figure style="width: 100%">
687+
![:img HeuDiConv workflow, 100%](https://raw.githubusercontent.com/nipy/heudiconv/master/figs/workflow.png)
688+
<figcaption>From <a href="https://github.com/nipy/heudiconv?tab=readme-ov-file#howto-101">HeuDiConv</a>;
689+
doi:![:doi](10.5281/zenodo.1012598)</figcaption>
690+
691+
]
692+
693+
---
694+
695+
# DICOM-to-BIDS: HeuDiConv
696+
697+
.boxed-content[
698+
699+
.no-bullet.large[
700+
* <i class="fa-solid fa-1"></i> &nbsp; Generate a **heuristic file**
701+
702+
* <i class="fa-solid fa-2"></i> &nbsp; Edit the **heuristic file**
703+
]
704+
705+
.small[
706+
```Python
707+
data = create_key('run-{item:03d}')
708+
709+
t1w = create_key('sub-{subject}/{session}/anat/sub-{subject}_{session}_T1w')
710+
711+
dwi = create_key('sub-{subject}/{session}/dwi/sub-{subject}_{session}_dir-AP_dwi')
712+
713+
# Save the RPE (reverse phase-encode) B0 image as a fieldmap (fmap). It will be used to correct
714+
# the distortion in the DWI
715+
fmap_rev_phase = create_key('sub-{subject}/{session}/fmap/sub-{subject}_{session}_dir-PA_epi')
716+
717+
fmap_mag = create_key('sub-{subject}/{session}/fmap/sub-{subject}_{session}_magnitude')
718+
719+
fmap_phase = create_key('sub-{subject}/{session}/fmap/sub-{subject}_{session}_phasediff')
720+
721+
# Even if this is resting state, you still need a task key
722+
func_rest = create_key('sub-{subject}/{session}/func/sub-{subject}_{session}_task-rest_run-01_bold')
723+
func_rest_post = create_key('sub-{subject}/{session}/func/sub-{subject}_{session}_task-rest_run-02_bold')
724+
```
725+
]
726+
727+
.no-bullet.large[
728+
* <i class="fa-solid fa-3"></i> &nbsp; Execute *HeuDiConv*
729+
]
730+
731+
]
732+
733+
---
734+
735+
# DICOM-to-BIDS: ReproIn + HeuDiConv
736+
737+
.no-bullet.large[
738+
* <i class="fa-solid fa-circle-chevron-right"></i> &nbsp; Just run *HeuDiConv* directly! *Heuristic file* is pre-defined.
739+
740+
* <i class="fa-solid fa-circle-question"></i> &nbsp; What if I **did not** follow *ReproIn* namings?
741+
]
742+
743+
--
744+
745+
.boxed-content.small[
746+
747+
``` Python
748+
# A dictionary containing fixes/remapping for sequence names per study.
749+
# Keys are md5sum of study_description from DICOMs, in the form of PI-Experimenter^protocolname
750+
# You can use `heudiconv -f reproin --command ls --files PATH
751+
# to list the "study hash".
752+
# Values are list of tuples in the form (regex_pattern, substitution).
753+
# If the key is an empty string "", it would apply to any study.
754+
protocols2fix: dict[str | re.Pattern[str], list[tuple[str, str]]] = {
755+
"": [ # <-- empty string means apply to whole study
756+
("anat-T1w_acq-mp2rage_run-01", "anat-mp2rage"),
757+
("_UNI_", "_acq-mp2rage__"),
758+
("_UNI-DEN", "_acq-denoised__"),
759+
("_INV", "_inv-"),
760+
("_T1_", "_acq-T1map__"),
761+
("fmap_acq-siemens", "fmap-phasediff"),
762+
("fmap-gre_acq-siemens", "fmap-phasediff"),
763+
("_acq-midRes", ""),
764+
("_acq-p6", ""),
765+
("_run-01", ""),
766+
]
767+
}
768+
```
769+
770+
]
771+
772+
---
773+
774+
# DICOM-to-BIDS: ReproIn + HeuDiConv
775+
776+
.left-column-mid[
777+
Our dataset's DICOM had some non-compliant names:
778+
.small[
779+
.pad-left[
780+
<i class="fa-solid fa-folder-open"></i> my_dataset/<br />
781+
.pad-left[<i class="fa-solid fa-folder-open"></i> sub-11]<br />
782+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 10 - anat-T1w_acq-mp2rage_run-01<mark>_UNI_Images</mark>.dicom]]<br />
783+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 11 - anat-T1w_acq-mp2rage_run-01<mark>_UNI-DEN</mark>.dicom]]<br />
784+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 12 - anat-T1w_acq-mp2rage_run-01<mark>_INV2</mark>.dicom]]<br />
785+
.pad-left[.pad-left[<i class="fa-solid fa-folder-open"></i> 16 - fmap-gre_acq-siemens_run-01/]]<br />
786+
.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 />
787+
.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 />
788+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 17 - <mark>fmap-gre</mark>_acq-siemens_run-01.dicom ]]<br />
789+
.pad-left[.pad-left[<i class="fa-solid fa-folder-open"></i> 18 - func-bold_acq-midRes_task-rest_run-01/ ]]<br />
790+
.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 />
791+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-ellipsis"></i>]]]<br />
792+
.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 />
793+
.pad-left[.pad-left[<i class="fa-solid fa-folder-open"></i> 20 - func-bold_acq-midRes_task-mixed_run-01/ ]]<br />
794+
.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 />
795+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-ellipsis"></i>]]]<br />
796+
.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 />
797+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 22 - anat-T2w_acq-p6_run-01.dicom]]<br />
798+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 7 - anat-T1w_acq-mp2rage_run-01<mark>_INV1</mark>.dicom]]<br />
799+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 8 - anat-T1w_acq-mp2rage_run-01<mark>_T1_Images</mark>.dicom]]<br />
800+
.pad-left[.pad-left[<i class="fa-solid fa-layer-group"></i> 9 - anat-T1w_acq-mp2rage_run-01<mark>_T1_Images</mark>.dicom]]<br />
801+
.pad-left[<i class="fa-solid fa-folder"></i> sub-14]<br />
802+
.pad-left[<i class="fa-solid fa-folder"></i> sub-15]<br />
803+
]
804+
]]
805+
806+
.right-column-mid.small[
807+
.pad-left[
808+
<i class="fa-solid fa-folder-open"></i> my_dataset/<br />
809+
.pad-left[<i class="fa-solid fa-file-lines"></i> CHANGES]<br />
810+
.pad-left[<i class="fa-solid fa-file-lines"></i> README]<br />
811+
.pad-left[<i class="fa-solid fa-paperclip"></i> dataset_description.json]<br />
812+
.pad-left[<i class="fa-solid fa-paperclip"></i> participants.json]<br />
813+
.pad-left[<i class="fa-solid fa-table"></i> participants.tsv]<br />
814+
.pad-left[<i class="fa-solid fa-paperclip"></i> scans.json]<br />
815+
.pad-left[<i class="fa-solid fa-folder-open"></i> sub-11]<br />
816+
.pad-left[.pad-left[<i class="fa-solid fa-folder-open"></i> anat/]]<br />
817+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_T2w.json]]]<br />
818+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_T2w.nii.gz]]]<br />
819+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_acq-denoised_T1w.json]]]<br />
820+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_acq-denoised_T1w.nii.gz]]]<br />
821+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_acq-mp2rage_T1w.json]]]<br />
822+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_acq-mp2rage_T1w.nii.gz]]]<br />
823+
.pad-left[.pad-left[<i class="fa-solid fa-folder-open"></i> fmap/]]<br />
824+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_magnitude1.json]]]<br />
825+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_magnitude1.nii.gz]]]<br />
826+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_magnitude2.json]]]<br />
827+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_magnitude2.nii.gz]]]<br />
828+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_phasediff.json]]]<br />
829+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_phasediff.nii.gz]]]<br />
830+
.pad-left[.pad-left[<i class="fa-solid fa-folder-open"></i> func/]]<br />
831+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_task-mixed_bold.json]]]<br />
832+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_task-mixed_bold.nii.gz]]]<br />
833+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-table"></i> sub-11_task-mixed_events.tsv]]]<br />
834+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-paperclip"></i> sub-11_task-rest_bold.json]]]<br />
835+
.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_task-rest_bold.nii.gz]]]<br />
836+
.pad-left[.pad-left[<i class="fa-solid fa-table"></i> sub-11_scans.tsv]]<br />
837+
.pad-left[<i class="fa-solid fa-folder"></i> sub-14]<br />
838+
.pad-left[<i class="fa-solid fa-folder"></i> sub-15]<br />
839+
]
840+
]
841+
842+
<i class="fa-solid fa-circle-right" style="margin-top: 20%; font-size: 1.7em"></i>
666843

667844
---
668845

0 commit comments

Comments
 (0)