Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Harmonize PET tracers handling (ML / DL / Stats) #137

Merged
merged 51 commits into from
Nov 3, 2020
Merged

Harmonize PET tracers handling (ML / DL / Stats) #137

merged 51 commits into from
Nov 3, 2020

Conversation

alexandreroutier
Copy link
Contributor

@alexandreroutier alexandreroutier commented Oct 20, 2020 •
edited
Loading

Follows PR #129.

After this PR, handling of PET tracers will be the same across Clinica pipelines (acq_label / suvr_reference_region / optional use_pvc_data).

alexandreroutier and others added 27 commits October 20, 2020 15:12
@alexandreroutier
Remove lower/upper case of PET tracer
17adcc8
@alexandreroutier
Harmonize ml-prepare-data w.r.t. PET tracers
29dd415
@alexandreroutier
Use -acq/--acq_label flag instead of -al/--acq_label
69eda8c
@alexandreroutier
Add path option to get_file_from_server
596c570
@alexandreroutier
Harmonize PET tracers handling (stats-surface)
b0190a9
@alexandreroutier
Add pet_volume_normalized_suvr_pet function
b3f4900
@alexandreroutier
Add group_label to pet_volume_normalized_suvr_pet
670597f
@alexandreroutier
Improve pet_volume_normalized_suvr_pet description
6586ecc
@alexandreroutier
Harmonize PET tracers handling (stats-volume)
317a55f
@alexandreroutier
Use f-string for custom-pipeline/pet-* pipeline CLI
ed7bdae
@alexandreroutier
Set False as default value for use_pvc_data
c0fbe5b
@alexandreroutier
Harmonize PET tracers handling (ml-spatial-svm)
2e83b7b
@alexandreroutier
Immprove readibility of get_pet_surface_custom_file
10b4551
@alexandreroutier
Document get_file_from_server
a91fe91
@alexandreroutier
Centralize list of SUVR regions
9bf26b4
@alexandreroutier
Format SUVR utils
27ecf51
@alexandreroutier
Add PET_Introduction page
1b44532
@alexandreroutier
Unify how volume atlases are handled
0ff0dce
@alexandreroutier
Update region_based_io.py
478029d 
get_caps_pet_list function was removed. This function is obsolete (it contained the attempt of defining an analysis-series ID abandoned in 2016-17) and is not used in Clinica. It is likely to be replaced by CAPSTSVBasedInput now.
@alexandreroutier
Update voxel_based_io.py
86423f9
@alexandreroutier
Harmonize PET tracers handling (ML modules)
8264d11
@alexandreroutier
Remove get_caps_t1_list/get_caps_pet_list
e18a076 
These functions are obsolete and are replaced by CAPSInputs classes in input.py
@alexandreroutier
Fix how CAPS files are grabbed
25df672
@alexandreroutier
Add missing default keys to CAPSVertexBasedInput
83c758a
@alexandreroutier
Harmonize PET tracers handling (ML-Workflows modules)
d144358
@alexandreroutier
Remove cprint() displaye used for debug
2ca7ce5
@alexandreroutier @nburgos
Improve description of --acq_label flag
7ec3c67 
Co-authored-by: Ninon Burgos <ninon.burgos@gmail.com>
@alexandreroutier alexandreroutier marked this pull request as ready for review October 23, 2020 12:21
alexandreroutier and others added 22 commits October 23, 2020 16:24
@alexandreroutier @nburgos
Improve PET Introduction page
ec9699f 
Co-authored-by: Ninon Burgos <nburgos@users.noreply.github.com>
@alexandreroutier
Explain how to add new volume atlas to Clinica
39c9a43
@alexandreroutier @nburgos
Update PET-Volume page w.r.t. tracers harmonization
b2bb50e 
Co-authored-by: Ninon Burgos <nburgos@users.noreply.github.com>
@alexandreroutier
Update PET-Surface page w.r.t. tracers harmonization
c601f2f
@alexandreroutier @nburgos
Improve CLI description of statistics-volume
61ef52c 
Co-authored-by: Ninon Burgos <nburgos@users.noreply.github.com>
@alexandreroutier
Update Stats-Volume page w.r.t. tracers harmonization
44261c3
@alexandreroutier
Generalize SUVR region for amyloid tracer
9fe2028
@nburgos
Proofreading
14556e5
@nburgos
Proofreading
1584be4
@nburgos
Proofreading
83b09f0
@nburgos
Proofreading
17c8c78
@alexandreroutier
Update ML-SpatialSVM page w.r.t. tracers harmonization
df621d8
@alexandreroutier
Enforce <participant_id>/<session_id> wording
c81d0d4
@alexandreroutier
Update Stats-Surface page w.r.t. tracers harmonization
66dbf8e
@alexandreroutier
Update ML page w.r.t. tracers harmonization
58bba01
@alexandreroutier
Update index.md
100f54f
@nburgos
Proofreading
423063f
@nburgos
Proofreading
128f18c
@nburgos
Proofreading
efb7032
@nburgos
Proofreading
82e527c
@nburgos
Proofreading
3411629
@nburgos
Proofreading
047e037
nburgos
nburgos reviewed Oct 28, 2020
View reviewed changes
Copy link
Contributor

@nburgos nburgos left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I checked all the wiki pages and made modifications when needed. Should be all good now.

mdiazmel
mdiazmel reviewed Oct 29, 2020
View reviewed changes
Copy link
Collaborator

@mdiazmel mdiazmel left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks @alexandreroutier,
Code readability has improved a lot with these changes!
A couple suggestions before merging.

clinica/utils/inputs.py Outdated Show resolved Hide resolved
clinica/utils/inputs.py Outdated Show resolved Hide resolved
@alexandreroutier
Copy link
Contributor Author

Thanks @alexandreroutier,
Code readability has improved a lot with these changes!
A couple suggestions before merging.

Hi!

Thanks for the feedback, I addressed the comments in 022b72e :)

I think this can now be merged.

@mdiazmel
Copy link
Collaborator

mdiazmel commented Nov 3, 2020

Hi @alexandreroutier ,
I propose to do a "squash and merge" for this PR, if you're agree.

@mdiazmel mdiazmel merged commit 34b57ca into aramis-lab:dev Nov 3, 2020
@alexandreroutier alexandreroutier deleted the pet_tracers_2 branch December 9, 2020 09:06
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@mdiazmel mdiazmel mdiazmel left review comments

@nburgos nburgos nburgos left review comments

Assignees
No one assigned
Labels
doc Documentation (wiki, source code, etc.) pipeline
Projects
None yet
Milestone
0.4.0
Development

Successfully merging this pull request may close these issues.
3 participants
@alexandreroutier @mdiazmel @nburgos