ds000001 example processed with SPM #309

cmaumet · 2022-03-18T16:11:16Z

This PR includes an example of BIDS-derivatives dataset: ds000001 processed using SPM (using code available in https://github.com/NISOx-BDI/Software_Comparison/tree/bids_derivatives).

This dataset will be used as an example use-case for BEP028 (provenance)

README
dataset_description.json

Remi-Gau · 2022-03-19T11:38:05Z

Couple of comments on the preprocessed data only as BIDS has nothing official to say on stats output (yet).

Also this is an example of derivative data, so I might be extra annoying to make it "extra BIDS compliant" because it could definitely help implementing validation later on. Feel free to push back on my nitpicking.

Should the derivatives include the raw files? (IMHO: no)

I know that this is a very SPM thing to do but I feel this goes against the modularisation of "raw" and "derivatives" that BIDS tends to promote. Also this also leads to data duplication.

ds000001-spm/sub-01/anat
├── sub-01_from-T1w_to-IXI549Space_mode-image_xfm.nii.gz
├── sub-01_label-T1w_segparam.mat
├── sub-01_space-individual_desc-biascor_T1w.nii.gz
├── sub-01_space-individual_desc-skullstripped.gz
├── sub-01_space-individual_label-CSF_probseg.nii.gz
├── sub-01_space-individual_label-GM_probseg.nii.gz
├── sub-01_space-individual_label-WM_probseg.nii.gz
├── sub-01_space-IXI549Space_desc-preproc_T1w.nii.gz
└── sub-01_T1w.nii.gz                                                         <-- original raw file?

Mix of .nii and .nii.gz

find ds000001-spm/ -name '*.nii' shows that subject 15 and 16 (and few others) have .nii files while most others have .nii.gz.

Might be better to make everything .nii.gz.

missing sidecar JSON

Only highlighting the missing REQUIRED bits.

For preprocessed data, it should be mentioned if they are skullstripped or not
https://bids-specification.readthedocs.io/en/latest/05-derivatives/03-imaging.html#preprocessed-coregistered-andor-resampled-volumes

When using the individual-space, the reference MUST me mentoned:
https://bids-specification.readthedocs.io/en/latest/05-derivatives/02-common-data-types.html#examples_1

REQUIRED fields for the RAW should be propagated to the derivatives:
https://bids-specification.readthedocs.io/en/latest/05-derivatives/01-introduction.html#metadata-conventions

In practice this mostly means TaskName and RepetitionTime for the func bold timeseries.

Remi-Gau · 2022-03-19T12:31:43Z

Also added some 'tick box' in the top message for other things TODO

ds000001-spm/dataset-description.json

Co-authored-by: Remi Gau <[email protected]>

cmaumet · 2022-03-21T14:51:52Z

Thanks a bunch @Remi-Gau!

The previous commits includes:

Deletion of raw anat and func files
All nifti files in .nii.gz
Adding missing README + dataset_description.json

I'll work on the JSON files next!

Remi-Gau · 2022-03-21T14:58:31Z

I'll work on the JSON files next!

Suspect you can make your life easier by using the inheritance principle for many of the bold files.

effigies · 2022-04-19T14:32:57Z

Is it possible to submit a small subset of subjects? 2000+ files is hard on the browser, so I can't really review what's in here.

Remi-Gau · 2022-04-24T08:40:28Z

ds000001-spm/dataset-description.json

+    "Name": "SPM - Software Comparison workflow",
+    "BIDSVersion": "1.4.0",
+    "DatasetType": "derivative",
+    "License": "This dataset is made available under the Public Domain Dedication and License \nv1.0, whose full text can be found at \nhttp://www.opendatacommons.org/licenses/pddl/1.0/. \nWe hope that all users will follow the ODC Attribution/Share-Alike \nCommunity Norms (http://www.opendatacommons.org/norms/odc-by-sa/); \nin particular, while not legally required, we hope that all users \nof the data will acknowledge the OpenfMRI project and NSF Grant \nOCI-1131441 (R. Poldrack, PI) in any publications."


Suggested change

"License": "This dataset is made available under the Public Domain Dedication and License \nv1.0, whose full text can be found at \nhttp://www.opendatacommons.org/licenses/pddl/1.0/. \nWe hope that all users will follow the ODC Attribution/Share-Alike \nCommunity Norms (http://www.opendatacommons.org/norms/odc-by-sa/); \nin particular, while not legally required, we hope that all users \nof the data will acknowledge the OpenfMRI project and NSF Grant \nOCI-1131441 (R. Poldrack, PI) in any publications."

"License": "This dataset is made available under the Public Domain Dedication and License \nv1.0, whose full text can be found at \nhttp://www.opendatacommons.org/licenses/pddl/1.0/. \nWe hope that all users will follow the ODC Attribution/Share-Alike \nCommunity Norms (http://www.opendatacommons.org/norms/odc-by-sa/); \nin particular, while not legally required, we hope that all users \nof the data will acknowledge the OpenfMRI project and NSF Grant \nOCI-1131441 (R. Poldrack, PI) in any publications."

Suggested change

"License": "This dataset is made available under the Public Domain Dedication and License \nv1.0, whose full text can be found at \nhttp://www.opendatacommons.org/licenses/pddl/1.0/. \nWe hope that all users will follow the ODC Attribution/Share-Alike \nCommunity Norms (http://www.opendatacommons.org/norms/odc-by-sa/); \nin particular, while not legally required, we hope that all users \nof the data will acknowledge the OpenfMRI project and NSF Grant \nOCI-1131441 (R. Poldrack, PI) in any publications."

"License": "This dataset is made available under the Public Domain Dedication and License \nv1.0, whose full text can be found at \nhttp://www.opendatacommons.org/licenses/pddl/1.0/. \nWe hope that all users will follow the ODC Attribution/Share-Alike \nCommunity Norms (http://www.opendatacommons.org/norms/odc-by-sa/); \nin particular, while not legally required, we hope that all users \nof the data will acknowledge the OpenfMRI project and NSF Grant \nOCI-1131441 (R. Poldrack, PI) in any publications.",

missing comma

Remi-Gau

hey @cmaumet

had a chat with the bids maintainers on our last meeting.

A) Could you only include a couple of subjects in the dataset and not all of them ?

Because:

it makes it hard to review,
after the second subject it gets redundant for an example,
we expect a growing number of derivatives dataset examples in the coming months / years so keeping of them to a small number of files is going to be important for long term mantenance

It is possible to mention this in the README and to point to where the full dataset with non truncated data can be found.

Several points that will help this dataset more valid as derivatives

B) Could the SCRIPTS folder be renamed code (one of the allowed folders in the root of a BIDS directory)?

C) batch_rename.mat should probably be moved in that code folder.

D) the ONSETS/*.mat (I suspect they contain the Names, Onsets, Duration required by SPM for model specification) could probably be moved somewhere else:

within code?
or each .mat``file could be moved in the level1` folder of each subject (can be useful if there are several models to keep those onsets files "close" to the stats results they relate to) ?

Remi-Gau · 2022-04-24T08:41:14Z

ds000001-spm/task-balloonanalogrisktask_bold.json

@@ -0,0 +1,3 @@
+{
+  "SkullStripped": false,


Suggested change

"SkullStripped": false,

"SkullStripped": false

Remi-Gau

missing T1w suffix and .nii for some files

sub-*_space-individual_desc-skullstripped.gz -->
sub-*_space-individual_desc-skullstripped_T1w.nii.gz

Remi-Gau · 2022-04-24T10:26:46Z

trying to come up with a decent .bidsignore to make things BIDS derivatives compatible if we removed the .SKIP_VALIDATION and had a validator that can handle derivatives.

distinguishing:

valid BIDS derivatives files (currently described in the specs) that by definition are not in the .bidsignore
BIDS derivatives files described in BEP in the bidsingore for now
typical SPM flles whose name can be bidsiied without breaking SPM internal machinery
typical SPM flles whose name CANNOT be bidsiied without breaking SPM internal machinery

Suggested .bidsignore

### SPM specific output 

## BIDSified filenames

# anat

# deformation fields not supported yet (see BEP 14 https://bids.neuroimaging.io/bep014)
*xfm.nii.gz

# segmentation parameters
sub-*/anat/sub-*_label-T1w_segparam.mat

# func

# realignment parameters
sub-*/func/sub-*_task-*_desc-confounds_regressors.txt

## non BIDSified names (renaming those would break SPM internal machinery)

# stats

SPM.mat
beta_*.nii*
RPV.nii*
ResMS.nii*
mask.nii*
con_*.nii*
spmT_*.nii*
spmF_*.nii*

*nidm.zip    # filename could be bidsified
*.pdf        # filename could be bidsified
*.ps         # filename could be bidsified

@cmaumet

I am having second thought on the Might be better to make *everything* .nii.gz.

For example zipping beta*.nii.gz will make SPM scream. From a data management perspective having .gz is preferable. As a SPM user having to unzipping things before doing stats is inconvenient.

What kind of examples should we set ?

Remi-Gau · 2022-04-24T10:28:28Z

@effigies would having this kind of .bidsignore help non-SPMers review this PR?

Remi-Gau · 2022-05-16T19:27:49Z

Random thought:

sub-01_task-balloonanalogrisktask_run-01_desc-confounds_regressors.txt

should probably be

sub-01_task-balloonanalogrisktask_run-01_motion.txt

according to the BEP on funcitonal derivatives: bids-standard/bids-specification#519

ideally it should even be a TSV files with proper headers

cmaumet added 2 commits March 18, 2022 17:04

ds000001 example processed w/ spm

d3bc575

skip validation

c19f316

cmaumet added 3 commits March 21, 2022 15:23

add README and dataset_description

7cfab41

remove original anat files

b2001bd

remove original func files

500cf32

Remi-Gau reviewed Mar 21, 2022

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Co-authored-by: Remi Gau <[email protected]>

omar-rifai mentioned this pull request Apr 19, 2022

Add output from clinica t1freesurfer pipeline #313

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cmaumet added 2 commits April 19, 2022 15:54

.nii > .nii.gz

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sidecar json skullstripped bold files

9b75477

Remi-Gau reviewed Apr 24, 2022

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Remi-Gau requested changes Apr 24, 2022

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Remove sub-03 to sub-16

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ds000001 example processed with SPM #309

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ds000001 example processed with SPM #309

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