Created 'derivatives' folder with processed MPM output #38

lazaral · 2019-04-11T11:24:03Z

No description provided.

agahkarakuzu · 2019-04-11T12:24:08Z

@lazaral thanks! Small correction:

MTmap --> MTsat (magnetization transfer saturation index map)

Another concern regarding field maps, should we put them in the fmap folder @KirstieJane ?

lazaral · 2019-04-11T13:12:21Z

Good point, thank you @agahkarakuzu! The other maps are R1map R2starmap etc. - shall I go for "MTsatmap"?

I was also in doubt about the field maps as they're not "raw" data but they're also not the main output...

Gilles86 · 2019-04-11T13:22:46Z

@lazaral, great work!

Could you restructure the ds-04 a bit more, making a very clear distinction between derivatives and sourcedata? To be compeltely BIDSy, it should be something like

ds-04/derivatives/sub-01/anat/*_*map.nii.gz for derivatives
and
ds-04/sourcedata/sub-01/anat/*_*w.nii.gz for sourcedata

agahkarakuzu · 2019-04-11T13:24:21Z

@lazaral IMO we can keep this one as MTsat and let the R2starmap be the exceptionally long one, unless other people feel strongly otherwise :)

lazaral · 2019-04-11T13:37:20Z

@Gilles86 thank you, yes happy to restructure the folders!
Btw what do you think of the other examples? I noticed that there the maps are also just in an 'anat' folder - should I move them to 'derivatives' and restructure the other 3 example datasets too?

Gilles86 · 2019-04-11T13:42:27Z

Yes! Would be great if you could do that. Otherwise I can also give it a shot.

lazaral · 2019-04-11T13:44:04Z

Great, restructuring all the examples now :)

lazaral · 2019-04-11T13:50:32Z

@lazaral thanks! Small correction:

MTmap --> MTsat (magnetization transfer saturation index map)

Another concern regarding field maps, should we put them in the fmap folder @KirstieJane ?

@agahkarakuzu I think the point made by @Gilles86 on derivatives being a higher-level folder might solves this problem, as we can put the field maps in derivatives/sub-01/fmap/ ... curious to hear if @KirstieJane also agrees?

…ster folders Fixed small inconsistency in ds-01 (missing T2starmap.nii.gz file) Changed 'MTmap' to 'MTsat' in ds-04

lazaral · 2019-04-11T14:14:03Z

@Gilles86 Done! It's now added to the pull request :)

KirstieJane · 2019-04-15T19:59:27Z

@lazaral, great work!

Could you restructure the ds-04 a bit more, making a very clear distinction between derivatives and sourcedata? To be compeltely BIDSy, it should be something like
* `ds-04/derivatives/sub-01/anat/*_*map.nii.gz` for derivatives
  and

* `ds-04/sourcedata/sub-01/anat/*_*w.nii.gz` for sourcedata

Hey folks - I don't think this is quite right. sourcedata is for the stuff that comes off the scanner. The "bidsified" raw data (as in the raw data in BIDS format) should be in the same level as the derivatives directory: https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#source-vs-raw-vs-derived-data.

So while the derivatives data in this PR are correct, I think the raw data should have the /sourcedata folder removed from the path.

eg:

ds-04/sub-01/anat/*_*w.nii.gz`

I'll ping a PR to @lazaral's branch to show what I mean 😃

KirstieJane · 2019-04-15T20:06:19Z

Another concern regarding field maps, should we put them in the fmap folder @KirstieJane ?

@agahkarakuzu I think the point made by @Gilles86 on derivatives being a higher-level folder might solves this problem, as we can put the field maps in derivatives/sub-01/fmap/ ... curious to hear if @KirstieJane also agrees?

Heya - the field maps should go in the fmap folder I think. It is in the top level folder (neither sourcedata nor derivatives as above). Here's the current specification: https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#fieldmap-data

I think we need to update that section with an anatomical example. This conversation is already happening at #40.

[EDIT] Just as a quick question because I might have missed something. Why would the field maps go in the derivatives folder? Are they derived, as in, are they calculated off the scanner?

lazaral · 2019-04-16T12:51:57Z

@KirstieJane all makes sense - about the fields maps, my understanding is that with MPM both the B0 and B1+ field are calculated off the scanner in hMRI but others might be able to confirm.

Move example RAW data from SOURCE data & add (only one) derivatives pipeline folder

…ative folder; markdown file to introduce the Examples branch

lazaral · 2019-04-19T14:45:11Z

I've implemented some of the changes we've discussed on Wednesday - if people would like to have a look, any feedback is appreciated :)

(p.s. note that the FLASH/MEGRE and MPM suffices are still inconsistent, but have been fixed in other pull requests... not sure what the best thing to do is, but I have made a note of the inconsistencies in the current pull request so I'm happy to fix them manually here if helpful)

KirstieJane

Just a couple of comments addressing #46.

Haven't pulled to machine to check names of pipelines etc....will do soon!

KirstieJane · 2019-04-19T15:41:57Z

examples/MEGRE_multiecho/dataset_description.json

@@ -5,5 +5,5 @@
        "Kirstie Whitaker",
        "Gilles de Hollander"
    ],
-    "Description": "This virtual dataset is collected using a single FLASH sequence, which yields multiple images, corresponding to different echo times. This data has been used to calculate a quantitative susceptibility map, as well as a T2* map."
+    "Description": "This virtual dataset is collected using a single MEGRE sequence, which yields multiple images, corresponding to different echo times. This data has been used to calculate a quantitative susceptibility map, as well as a T2* map."


This is a great change ✅

This is what I was thinking of when I said add the information to the dataset_description.json file - adding the text you have describing the dataset in the BEP001_examples.md file to the json itself 😄

KirstieJane · 2019-04-19T15:42:27Z

examples/BEP001_examples.md

+You can find more about the BEP001 addition to the BIDS standard, and the rationale for the additions/changes that it brings to the BIDS format, here: https://github.com/bids-standard/bep001.
+
+ *The datasets in this branch contain empty data files, which might be useful for building simple software tests. 
+ The current branch may eventually be merged with the bids-examples branch of the main bids-standard repo: https://github.com/bids-standard/bids-examples, in which case this disclaimer will be redundant.*


KirstieJane · 2019-04-19T15:44:44Z

examples/BEP001_examples.md

+This is a sample dataset from an MP2RAGE sequence with two inversion times, and, for the second inversion time, 4 different echoes.
+
+## Example 4: MultiParameter Mapping (MPM) dataset
+This is a sample dataset from a MultiParameter Mapping (MPM) sequence (as per Weiskopf et al., 2013), which yields multi-echo FLASH scans that are predominantly T1-, PD-, or MT-weighted by changing repetition time and flip angle.


Maybe add a couple of sentences here about the fact that we don't CALL them FLASH scans because they were conceptually grouped together.

Suggested change

This is a sample dataset from a MultiParameter Mapping (MPM) sequence (as per Weiskopf et al., 2013), which yields multi-echo FLASH scans that are predominantly T1-, PD-, or MT-weighted by changing repetition time and flip angle.

This is a sample dataset from a MultiParameter Mapping (MPM) sequence (as per Weiskopf et al., 2013), which yields multi-echo FLASH scans that are predominantly T1-, PD-, or MT-weighted by changing repetition time and flip angle.

Note that the raw data for these scans are not called "FLASH" in their sufficies, rather they are grouped together with the "MPM" suffix and the "acq" tag is used to clarify which weightings the scans are highlighting.

Thank you @KirstieJane ! I've integrated the recommendation and added a small comment on FLASH/MEGRE just to avoid people getting confused by seeing the mention of FLASH - though it might be overkill, so I can also take that bit away.

Note that the raw data for these scans are not called "FLASH" (or MEGRE, following our recommended vendor-neutral notation) in their suffices, rather they are grouped together with the "MPM" suffix and the "acq" tag is used to clarify which weightings the scans are highlighting.

…he MPM example

Gilles86

Are the B1minus maps really B1 minus maps?!

Example update from Master

… lazaral-master

Gilles86 · 2019-07-25T14:31:13Z

So I heavily refactored the examples data in this branch
https://github.com/Gilles86/bep001/tree/examples

Somehow, I cannot push it to lazaral/master:

> git push -u lazaral master
To github.com:lazaral/bep001.git
 ! [rejected]        master -> master (non-fast-forward)
error: failed to push some refs to 'git@github.com:lazaral/bep001.git'
hint: Updates were rejected because a pushed branch tip is behind its remote
hint: counterpart. Check out this branch and integrate the remote changes
hint: (e.g. 'git pull ...') before pushing again.
hint: See the 'Note about fast-forwards' in 'git push --help' for details.

Which is weird because when I do

> fetch lazaral master
> git merge lazaral/master

It says

Already up to date.

Anyone has a clue what's wrong here? @KirstieJane ?

Gilles86 · 2019-07-25T14:35:31Z

Then, @lazaral, could you have a look again at the MPM-examples?

Some issues to look into:

Why is there a fmap-derivatives folder?
A given file can have only one relevant sidecar-json in the same folder. So You can't have and sub-01_acq-MTon_MPM.json and sub-01_echo-1_acq-MToff_MPM.json. You will have to put all the relevant metadata in sub-01_echo-1_acq-MToff_MPM.json only. This was wrong in the MP2RAGE-examples as well. Maybe have a look in https://github.com/Gilles86/bep001/tree/examples to see how I solved it.
Why do the anat MPM-files all have the same echo times?

lazaral · 2019-07-25T17:26:30Z

@Gilles86 thank you for the work and suggestions - I think I need some further clarifications :)

The B1 and B0 maps from MPM are an output of hMRI, rather than raw data from the scanner, so I thought we had decided in a previous meeting they'd go into derivatives because of that - should I move them out?
I kind of see what you mean in the MP2RAGE example but not sure I fully understand how that applies to the MPM example - MTon and MToff are entirely different scans so there is a nifti for each (MToff is what's called PDw in current hMRI/MPM wording).
Looking at your folder - do you mean that we shouldn't have a "master" json file (like sub-01_inv-1_MP2RAGE.json or sub-01_acq-T1w_MPM.json) for each contrast and rather just have the one json for each echo of each contrast? The way I process MPMs I don't get that "master" json file either, so I thought there was a specific reason why those additional "master" json files were there, but maybe there isn't :) happy to remove those "master" json files if that's not the case?
I was holding off adding extra details to the json files cause I thought the "real data example" of the MPMs will have that anyway. Is it useful to add realistic echo times at this stage? If so, should we also add other realistic fields to the json (e.g. flip angle etc.)?

…le; fixed suffices

lazaral · 2019-09-27T16:29:40Z

Quick summary of recent updates to this pull request: I've fixed a few small issue about file names that were raised at previous meetings, and added realistic jsons for all the niftis (anat and fmap files alike).

lazaral · 2019-09-27T16:30:44Z

One open question (@Gilles86 you might know?): previous versions of the MP2RAGE examples used to have a T1w scan, but I can't see it in the real example in OSF. Is that an error - should I remove it?

lazaral · 2019-09-27T16:32:37Z

Also, @agahkarakuzu MEGRE is not my specialty so the json files for that example are quite sparse sorry :) it might be nice to add some realistic details (e.g. repetition time and flip angle) if you have them at hand?

Created 'derivatives' folder with processed MPM output

05224b4

agahkarakuzu mentioned this pull request Apr 11, 2019

MPM example #34

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Restructured all 4 examples to have 'derivatives' and 'sourcedata' ma…

c0fe1ed

…ster folders Fixed small inconsistency in ds-01 (missing T2starmap.nii.gz file) Changed 'MTmap' to 'MTsat' in ds-04

Move example RAW data from SOURCE data

6b7d1c8

KirstieJane mentioned this pull request Apr 15, 2019

Move example RAW data from SOURCE data & add (only one) derivatives pipeline folder lazaral/bep001#1

Merged

Move derivatives files in ds-4 to an hmri pipeline folder

b140377

KirstieJane mentioned this pull request Apr 17, 2019

Agenda for April call | Wed 17 6pm / 5pm / 12noon / 9am #32

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7 tasks

lazaral added 2 commits April 19, 2019 14:33

Merge pull request #1 from KirstieJane/lazaral-master

6fb08a2

Move example RAW data from SOURCE data & add (only one) derivatives pipeline folder

Made clearer names for "ds-01/2/3/4" folders; pipeline names in deriv…

2cc6d07

…ative folder; markdown file to introduce the Examples branch

KirstieJane mentioned this pull request Apr 19, 2019

Make sure that all the names in our examples folder conform to spec and make sense #46

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KirstieJane reviewed Apr 19, 2019

View reviewed changes

Integrated suggested explanation for avoiding FLASH/MEGRE suffix in t…

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…he MPM example

Gilles86 reviewed May 15, 2019

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lazaral and others added 4 commits May 27, 2019 19:42

Merge pull request #2 from bids-standard/master

56d6370

Example update from Master

Fixed MPM and MEGRE examples, added sequence suffix to raw data

33f69cb

Merge branch 'master' of https://github.com/bids-standard/bep001 into…

6b36153

… lazaral-master

Merge branch 'lazaral-master'

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KirstieJane mentioned this pull request Sep 4, 2019

Notes from Sept 4 call, plan for Sept 18 call #70

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Alberto Lazari added 7 commits September 15, 2019 18:15

Removed extra json files to be compliant with the inheritance princip…

1ecae5d

…le; fixed suffices

added details to MPM scan jsons

b013898

updated json files for MP2RAGE_singleecho

0201643

updated json files for MP2RAGE_multiecho

ce73f3e

updated jsons for MPM fieldmaps

c4d09cf

created realistic json for MPM echoes

9183c89

MEGRE json expansion

9f83abd

lazaral mentioned this pull request Nov 12, 2019

Aligning MP2RAGE example folders with example datasets #81

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yarikoptic mentioned this pull request Mar 16, 2023

FOI: sample con/solidation report bids-standard/maintenance-tools#10

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Created 'derivatives' folder with processed MPM output #38

Created 'derivatives' folder with processed MPM output #38

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	This is a sample dataset from a MultiParameter Mapping (MPM) sequence (as per Weiskopf et al., 2013), which yields multi-echo FLASH scans that are predominantly T1-, PD-, or MT-weighted by changing repetition time and flip angle.
	This is a sample dataset from a MultiParameter Mapping (MPM) sequence (as per Weiskopf et al., 2013), which yields multi-echo FLASH scans that are predominantly T1-, PD-, or MT-weighted by changing repetition time and flip angle.
	Note that the raw data for these scans are not called "FLASH" in their sufficies, rather they are grouped together with the "MPM" suffix and the "acq" tag is used to clarify which weightings the scans are highlighting.

Created 'derivatives' folder with processed MPM output #38

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Created 'derivatives' folder with processed MPM output #38

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