Merge pull request #50 from CBICA/ag-dev

Ag dev force push
CBICA · Dec 11, 2024 · 99cbdbf · 99cbdbf
2 parents 6988e89 + af78dbb
commit 99cbdbf
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diff --git a/.dockerignore b/.dockerignore
@@ -1,5 +1,8 @@
 .github
+.git
 test
+test_data
+output_folder
 **/*.nii.gz
 build
 **/build

diff --git a/.gitignore b/.gitignore
@@ -179,5 +179,5 @@ test/test_output
 # ignore test dicom folder
 10089_short/
 
-# make sure no data go to the repo
-*.nii.gz
+## make sure no data go to the repo
+##*.nii.gz
diff --git a/Dockerfile b/Dockerfile
@@ -42,10 +42,11 @@ ARG MAMBA_DOCKERFILE_ACTIVATE=1
 ARG CUDA_VERSION
 
 COPY --chown=$MAMBA_USER:$MAMBA_USER requirements.txt /tmp/requirements.txt
+RUN grep -v -E '^(torch)' /tmp/requirements.txt > /tmp/requirements2.txt
 USER root
 RUN apt-get update && apt-get install -y python3-tk git
 USER $MAMBA_USER
-RUN pip install --verbose -r /tmp/requirements.txt && pip uninstall -y torch && pip install --verbose torch==2.3.1 --index-url https://download.pytorch.org/whl/cu${CUDA_VERSION}
+RUN pip install --verbose -r /tmp/requirements2.txt && pip uninstall -y torch && pip install --verbose torch==2.3.1 --index-url https://download.pytorch.org/whl/cu${CUDA_VERSION}
 RUN mkdir ~/dummyinput && mkdir ~/dummyoutput
 RUN git clone https://github.com/CBICA/PredCRD.git && cd PredCRD && pip install -e .
 RUN git clone https://github.com/CBICA/DLWMLS.git && cd DLWMLS && pip install -e . && DLWMLS -i ~/dummyinput -o ~/dummyoutput

diff --git a/TestData/README.txt b/TestData/README.txt
diff --git a/requirements.txt b/requirements.txt
@@ -3,11 +3,11 @@ spare-scores
 NiChartHarmonize
 DLICV
 DLMUSE
-NiChart_DLMUSE
+NiChart_DLMUSE>=1.0.9
 DLWMLS @ git+https://github.com/CBICA/DLWMLS
 
 # general python dependencies
-torch>=2.2.1,<=2.3.1
+torch==2.3.1
 argparse
 nibabel
 pulp==2.7.0
@@ -18,7 +18,9 @@ sphinx
 streamlit==1.39.0
 st_pages==1.0.1
 streamlit_plotly_events
+streamlit-base-extras
 chart_studio
 Jinja2
 plotly-express
 stqdm
+pyjwt
diff --git a/resources/centiles/istag_centiles_CN_ICV_Corrected.csv b/resources/centiles/istag_centiles_CN_ICV_Corrected.csv
@@ -1,77 +1,77 @@
 VarName,Age,centile_5,centile_25,centile_50,centile_75,centile_95
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+ICV,92,1115156.40493202,1256648.17741348,1350413.27072996,1441005.11349639,1566534.82912498
+ICV,93,1109272.04983806,1252018.85537473,1345819.84363609,1435925.44516336,1560032.1366764
 TotalBrain,21,1272916.87633068,1295969.8205078,1310356.62136667,1323695.6541929,1341423.47254941
 TotalBrain,22,1271406.34476039,1294693.98843156,1309226.95328749,1322706.25918351,1340635.72154964
 TotalBrain,23,1269897.42595918,1293423.34486688,1308104.20181107,1321725.69832835,1339860.92600001

diff --git a/resources/lists/dict_var_categories.json b/resources/lists/dict_var_categories.json
@@ -31,7 +31,7 @@
         "FieldStrength"
     ],
     "MUSE-TopPicks": [
-        "DLICV",
+        "ICV",
         "TotalBrain",
         "GM",
         "WM",
@@ -195,7 +195,7 @@
         "TransverseTemporalGyrus_L"
     ],
     "MUSE-CompositeROIs": [
-        "DLICV",
+        "ICV",
         "TotalBrain",
         "GM",
         "WM",

diff --git a/resources/lists/prepare_data/prepare_dict_var_categories/input/varlist_MUSE-Composite.csv b/resources/lists/prepare_data/prepare_dict_var_categories/input/varlist_MUSE-Composite.csv
@@ -1,5 +1,5 @@
 VarName
-DLICV
+ICV
 TotalBrain
 GM
 WM

diff --git a/resources/lists/prepare_data/prepare_dict_var_categories/input/varlist_MUSE-Essential.csv b/resources/lists/prepare_data/prepare_dict_var_categories/input/varlist_MUSE-Essential.csv
@@ -1,5 +1,5 @@
 VarName
-DLICV
+ICV
 TotalBrain
 GM
 WM

diff --git a/resources/lists/prepare_data/prepare_dict_var_categories/output/dict_var_categories.json b/resources/lists/prepare_data/prepare_dict_var_categories/output/dict_var_categories.json
@@ -21,7 +21,7 @@
         "DX_Diabates"
     ],
     "MUSE-Essential": [
-        "DLICV",
+        "ICV",
         "TotalBrain",
         "GM",
         "WM",
@@ -185,7 +185,7 @@
         "TransverseTemporalGyrus_L"
     ],
     "MUSE-Composite": [
-        "DLICV",
+        "ICV",
         "TotalBrain",
         "GM",
         "WM",

diff --git a/resources/videos/nichart_vtutorial_smri_1.webm b/resources/videos/nichart_vtutorial_smri_1.webm
diff --git a/resources/videos/nichart_vtutorial_smri_2.webm b/resources/videos/nichart_vtutorial_smri_2.webm
diff --git a/src/viewer/pages/home.py b/src/viewer/pages/home.py
@@ -108,6 +108,5 @@ def set_pipeline() -> None:
         unsafe_allow_html=True,
     )
 
-
 # FIXME: For DEBUG
 utilst.add_debug_panel()
diff --git a/src/viewer/pages/pipeline_dlmuse.py b/src/viewer/pages/pipeline_dlmuse.py
@@ -12,7 +12,7 @@
 st.markdown(
     """
     # Structural MRI Biomarkers
-    ### Neuroimaging pipeline for computing AI biomarkers of disease and aging from T1-weighted MRI scan
+    ### Neuroimaging pipeline for computing AI biomarkers of disease and aging from T1-weighted MRI scans
     """
 )
-Original file line number
+Diff line change
@@ -1,5 +1,5 @@
     VarName
-    DLICV
+    ICV
     TotalBrain
     GM
     WM
@@ Expand Down @@