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Implementation of 5ttgen algorithms for neonatal data.#2393

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mblesac wants to merge 17 commits intoMRtrix3:devfrom
mblesac:master
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Implementation of 5ttgen algorithms for neonatal data.#2393
mblesac wants to merge 17 commits intoMRtrix3:devfrom
mblesac:master

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@mblesac mblesac commented Nov 8, 2021

Co-authored-by: Manuel Blesa Cabez mblesac@gmail.com
Co-authored-by: Paola Galdi paola.galdi@gmail.com

mblesac2 and others added 2 commits November 8, 2021 14:54
@mblesac @paola-g
Implementation of 5tt algorithm for neonatal data.
dc0a395 
Co-authored-by: Manuel Blesa Cabez <mblesac@gmail.com>
Co-authored-by: Paola Galdi <paola.galdi@gmail.com>
@mblesac @paola-g
Update of the neonatal 5tt algorithm to include the dHCP option
e528413 
Co-authored-by: Manuel Blesa <mblesac@gmail.com>
Co-authored-by: Paola Galdi <paola.galdi@gmail.com>
@Lestropie Lestropie self-assigned this Nov 11, 2021
@Lestropie Lestropie changed the base branch from master to dev November 11, 2021 00:49
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Lestropie commented Nov 11, 2021

@mblesac I modified the PR to propose the merge into the MRtrix3:dev branch: as per contribution guidelines, merges to master are only for critical bug fixes. This results in this PR showing a number of additional commits; these should disappear after I explicitly perform a merge of MRtrix3:master into MRtrix3:dev. After that I ideally need write access to your fork in order to perform some requisite cleanup.

@Lestropie Lestropie mentioned this pull request Nov 15, 2021
Merged
mblesac2 and others added 12 commits November 16, 2021 13:41
@mblesac @paola-g
Fix syntax errors
f65a394 
Co-authored-by: Manuel Blesa <mblesac@gmail.com>
Co-authored-by: Paola Galdi <paola.galdi@gmail.com>
@mblesac @paola-g
Remove histogram matching
a7f3188 
Co-authored-by: Manuel Blesa <mblesac@gmail.com>
Co-authored-by: Paola Galdi <paola.galdi@gmail.com>
@mblesac @paola-g
Neonatal algorithm split in two: neonatal_mcrib and neonatal_dhcp
246cfca 
Co-authored-by: Manuel Blesa <mblesac@gmail.com>
Co-authored-by: Paola Galdi <paola.galdi@gmail.com>
Renaming algorithms and modification of the dhcp (using path as an in…
db20d6a 
…put)

Manuel Blesa <mblesac@gmail.com>
Paola Galdi <paola.galdi@gmail.com>
@mblesac @paola-g
Addition of the option to use hard of soft segmentations to both neon…
7438c0d 
…atal algorithms

Co-authored-by: Manuel Blesa <mblesac@gmail.com>
Co-authored-by: Paola Galdi <paola.galdi@gmail.com>
@Lestropie
5ttgen dhcp: Code cleanup
9260baf 
- Ensure that input files are unique and unambiguous.
- Remove redundant logic across get_inputs() and execute() regarding use of hard segmentation.
- Simplify logic of primary conversion loop.
- Generate sub-cortical grey matter image from M-CRIB only once, rather than once per tissue; this should facilitate code execution without using the -force option.
@Lestropie
5ttgen: Revert names of new algorithms
fe7fe13
@Lestropie
5ttgen: pylint fixes for new algorithms
1bbb593
@paola-g
removed EN-DASH from reference
c48e69a
@paola-g
removed unicode char from refs
dc59419
@paola-g
updated docs with new 5ttgen commands
4757b77
@mblesac
Merge pull request #1 from mblesac/5ttgen_neonatal_rs
d7475aa 
Proposed code cleanup
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Lestropie commented Dec 3, 2021

@jdtournier: Would ideally like to add a dHCP subject to script_test_data in order to capture new ANTs dependencies in the containers. Any knowledge of license permissibility to upload there a stripped-down & downsampled dataset, or do you perhaps alternatively have a pilot dataset that could be used for that purpose?

@Lestropie Lestropie changed the title Implementation of 5tt algorithm for neonatal data. Implementation of 5ttgen algorithms for neonatal data. Jul 29, 2024
@Lestropie Lestropie force-pushed the dev branch 3 times, most recently from 70031c3 to 6bf4cec Compare August 26, 2025 08:11
@Lestropie Lestropie mentioned this pull request Oct 1, 2025
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Lestropie commented Oct 1, 2025

Superseded by #3193.

@Lestropie Lestropie closed this Oct 1, 2025
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