CBICA / niCHART

The neuro-imaging brain aging chart [niCHART] is a comprehensive solution to analyze standard structural and functional brain MRI data across studies. [niCHART] and the associated pre-processing tools implement computational morphometry, functional signal analysis, quality control, statistical harmonization, data standardization, interactive visual
https://cbica.github.io/niCHART/
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Implement new out-of-sample harmonization in NiBAx #206

Closed melhemr closed 2 years ago

melhemr commented 2 years ago

PR will update OOS harmonization in the GUI to use Combat-GAM

Requires neuroHarmonize PR package: python -m pip install -U git+https://github.com/rpomponio/neuroHarmonize@refs/pull/20/head

AbdulkadirA commented 2 years ago

@melhemr Thanks. The correct version of neuroHarmonize should be installed automatically:

diff --git a/pyproject.toml b/pyproject.toml
index 9537161..a215d8b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -71,11 +71,9 @@ requires = ['cycler==0.10.0',
 'matplotlib>=3.4.2',
 'nibabel==3.2.1',
 'numpy>=1.21',
-'neuroHarmonize==2.1',
+'git+https://github.com/rpomponio/neuroHarmonize@refs/pull/20/head#egg=neuroHarmonize',
 'pandas==1.3.4',
 'Pillow>=9.0.0',
-'poetry>=1.1.13',
-'poetry_core>=1.0.7',
 'pyparsing==2.4.7',
 'PyQt5>=5.15.4',
 'PyQt5_Qt5==5.15.2',
@@ -104,7 +102,7 @@ MarkupSafe = "2.0.1"
 matplotlib = "^3.4.2"
 nibabel = "^3.2.1"
 numpy = "^1.21"
-neuroHarmonize = "2.1"
+neuroHarmonize = { git = "https://github.com/rpomponio/neuroHarmonize.git", branch = "refs/pull/20/head" }
 pandas = "1.3.4"
 Pillow = "^9.0.0"
 poetry = "^1.1.13"
diff --git a/requirements.txt b/requirements.txt
index 7d62042..b02aae5 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,7 +3,7 @@ joblib==1.0.1
 matplotlib>=3.4.2
 nibabel==3.2.1
 numpy>=1.21
-neuroHarmonize==2.1
+git+https://github.com/rpomponio/neuroHarmonize@refs/pull/20/head
 pandas==1.3.4
 Pillow>=9.0.0
 poetry>=1.1.13