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Add new centiles; Add mni atlas image and seg #136

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Binary file added resources/atlases/muse/MNI152_1mm_LPS.nii.gz
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Binary file added resources/atlases/muse/MNI152_1mm_LPS_DLMUSE.nii.gz
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2 changes: 2 additions & 0 deletions resources/atlases/muse/MNI152_1mm_LPS_DLMUSE_Volumes.csv
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@@ -0,0 +1,2 @@
MRID,702,701,600,601,604,606,607,613,614,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,521,522,523,524,525,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,4,11,23,30,31,32,35,36,37,38,39,40,41,47,48,49,50,51,52,55,56,57,58,59,60,61,62,71,72,73,75,76,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,100,101,102,103,104,105,106,107,108,109,112,113,114,115,116,117,118,119,120,121,122,123,124,125,128,129,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207
MNI152_1mm_LPS,1834388.0,1675775.0,156792.0,889961.0,736228.0,439610.0,359382.0,437713.0,361371.0,15475.0,184013.0,75759.0,547803.0,47518.0,169777.0,278444.0,294927.0,23866.0,85651.0,37813.0,271866.0,24081.0,84073.0,141765.0,147374.0,10771.0,85724.0,37946.0,275937.0,23437.0,85704.0,136679.0,147553.0,9834.0,25255.0,21377.0,15076.0,262551.0,285252.0,47518.0,94980.0,74797.0,138227.0,140217.0,141192.0,153735.0,12702.0,10786.0,7456.0,130896.0,140970.0,24081.0,47128.0,36945.0,69985.0,71780.0,71081.0,76293.0,12553.0,10591.0,7620.0,131655.0,144282.0,23437.0,47852.0,37852.0,68242.0,68437.0,70111.0,77442.0,27463.0,17813.0,144119.0,51794.0,21362.0,35460.0,12058.0,12048.0,40787.0,42145.0,104562.0,33665.0,21202.0,105779.0,14211.0,13711.0,8841.0,71910.0,25451.0,10983.0,18050.0,6031.0,6266.0,20462.0,20400.0,53408.0,16577.0,10284.0,53205.0,7592.0,13752.0,8972.0,72209.0,26343.0,10379.0,17410.0,6027.0,5782.0,20325.0,21745.0,51154.0,17088.0,10918.0,52574.0,6619.0,909.0,2352.0,613.0,695.0,1274.0,1283.0,25720.0,4191.0,4143.0,66090.0,66082.0,19634.0,19569.0,5231.0,4873.0,422.0,343.0,9412.0,10428.0,2027.0,1983.0,5722.0,5881.0,10591.0,10786.0,6104.0,6369.0,5798.0,2993.0,3847.0,713.0,677.0,144282.0,140970.0,37852.0,36945.0,68437.0,71780.0,77442.0,76293.0,609.0,785.0,4252.0,3887.0,2759.0,2784.0,15475.0,6148.0,6962.0,5863.0,5877.0,2584.0,1988.0,13505.0,12733.0,4607.0,4942.0,5326.0,5174.0,6403.0,5991.0,2392.0,2421.0,2385.0,2306.0,3276.0,3036.0,10918.0,10284.0,2867.0,2898.0,8224.0,6831.0,15225.0,15708.0,10735.0,9467.0,2315.0,2569.0,6374.0,5779.0,2700.0,2897.0,23633.0,24627.0,5118.0,6668.0,4971.0,5331.0,1241.0,1039.0,4027.0,3608.0,9687.0,7715.0,17816.0,18408.0,2440.0,2494.0,5782.0,6266.0,4138.0,4630.0,1981.0,2265.0,4888.0,5309.0,15847.0,15538.0,3635.0,3610.0,3109.0,2964.0,2668.0,3503.0,12788.0,16179.0,3882.0,3823.0,2403.0,2677.0,16634.0,16003.0,2505.0,3056.0,1592.0,1684.0,18274.0,16557.0,5470.0,6649.0,11625.0,12635.0,4543.0,4469.0,13236.0,11861.0,8463.0,8453.0,11070.0,10636.0,4273.0,4792.0,1711.0,1859.0
16,769 changes: 16,769 additions & 0 deletions resources/reference_data/centiles/nichart_centiles_AD-All.csv
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16,239 changes: 16,239 additions & 0 deletions resources/reference_data/centiles/nichart_centiles_AD-Females.csv
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15,684 changes: 15,684 additions & 0 deletions resources/reference_data/centiles/nichart_centiles_AD-Males.csv
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22,424 changes: 22,424 additions & 0 deletions resources/reference_data/centiles/nichart_centiles_CN-All.csv
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22,424 changes: 22,424 additions & 0 deletions resources/reference_data/centiles/nichart_centiles_CN-Females.csv
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22,384 changes: 22,384 additions & 0 deletions resources/reference_data/centiles/nichart_centiles_CN-Males.csv
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91 changes: 91 additions & 0 deletions src/viewer/gui/utils_mriview.py
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Expand Up @@ -279,15 +279,106 @@ def show_img_slices(img, scroll_axis, sel_axis_bounds, orientation, wimg = None)
else:
st.image(img[:, :, slice_index], width=wimg)

def panel_view_seg_refplot(ptype):
'''
Panel to display segmented image overlaid on underlay image for the reference data
'''
logger.debug('Panel: View Segmentation for the Ref Plot')

ss = st.session_state
pdict = ss[ptype]

ylab = pdict['selected']['ylab']
# ylab = 'DL_MUSE_Volume_GM'


# Find roi indices
col_dict = pdict['data']['col_dict']
roi = col_dict.renamed_to_roi_index(ylab)

if roi is None:
logger.debug('ROI not found')
return
roi_indices = st.session_state.dicts['muse']['derived'].get(roi, [roi])
if roi_indices is None or len(roi_indices)<=0:
logger.debug('No ROI indices found')
return

tab1, tab2 = st.tabs(
[':material/visibility_off:', 'Options'],
on_change='rerun',
key='_tabs_mri_controls',
)

if tab2.open:
with tab2:
with st.container(border=True):
select_mriplot_settings(ptype)

if pdict['settings']['mri_ulay'] is None:
st.toast('Underlay image not found!')
return

if pdict['settings']['mri_olay'] is None:
st.toast('Overlay image not found!')
pdict['settings']['mri_flag_olay'] = False
st.rerun()

# Show images
with st.container(border=True):
try:
img, mask, img_masked = prep_image_and_olay(
pdict['settings']['mri_ulay'],
pdict['settings']['mri_olay'],
list_rois=roi_indices,
crop_to_mask=pdict['settings']['mri_flag_crop']
)
except Exception as exc:
st.warning(f'Could not read image files! {exc}')
st.write(pdict['settings']['mri_ulay'])
st.write(pdict['settings']['mri_olay'])
st.write(pdict['settings'])
return

img_bounds = detect_mask_bounds(mask)

pdict['settings']['mri_orient'] = ['axial']
nviews = len(pdict['settings']['mri_orient'])
if nviews == 0:
return
cols = st.columns(nviews)
for i, sel_orient in enumerate(pdict['settings']['mri_orient']):
with cols[i]:
ind_view = img_views.index(sel_orient)
if pdict['settings']['mri_olay'] is None or pdict['settings']['mri_flag_olay'] is False:
show_img_slices(
img, ind_view, img_bounds[ind_view, :], sel_orient
)
else:
show_img_slices(
img_masked, ind_view, img_bounds[ind_view, :], sel_orient
)





def panel_view_seg(ptype):
'''
Panel to display segmented image overlaid on underlay image
'''
logger.debug('Panel: View Segmentation')

if ptype == 'ref_plots':
panel_view_seg_refplot(ptype)
return

ss = st.session_state
pdict = ss[ptype]

# logger.debug(pdict)
# st.write(pdict)

mrid = pdict['selected']['mrid']
ylab = pdict['selected']['ylab']

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4 changes: 4 additions & 0 deletions src/viewer/gui/utils_plots.py
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Expand Up @@ -129,6 +129,10 @@ def select_centile_type(ptype):

list_types = pdict['settings'].get('cent_types', [])
vname = f"{ptype}.data.cent_type"

# st.write(pdict)
# st.write((f"Centile types: {list_types}") )

utilwd.my_selectbox(
vname, list_types, 'Centile Type'
)
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27 changes: 23 additions & 4 deletions src/viewer/gui/utils_session.py
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Expand Up @@ -21,8 +21,9 @@ def init_plots():
}

# Set plot data params
pref = os.path.join(st.session_state.paths['centiles'], 'nichart_centiles_dlmuse')
ctype = 'CN'
pref = os.path.join(st.session_state.paths['centiles'], 'nichart_centiles')
# ctype = 'dlmuse_CN'
ctype = 'CN-All'
dtmp = {
"cent_type": ctype,
"cent_path": pref,
Expand Down Expand Up @@ -137,7 +138,20 @@ def init_ref_plots():
plots = init_plots()

# Set centile types
plots['settings']['cent_types'] = ["None", "CN", "CN-Males", "CN-Females"]
# plots['settings']['cent_types'] = ["CN", "CN-Males", "CN-Females"]
plots['settings']['cent_types'] = [
"None",
"CN-All", "CN-Males", "CN-Females",
"AD-All", "AD-Males", "AD-Females",
]
plots['settings']['mri_ulay'] = os.path.join(
st.session_state.paths['resources'], 'atlases',
'muse', 'MNI152_1mm_LPS.nii.gz'
)
plots['settings']['mri_olay'] = os.path.join(
st.session_state.paths['resources'], 'atlases',
'muse', 'MNI152_1mm_LPS_DLMUSE.nii.gz'
)

# Save in session state
st.session_state['ref_plots'] = plots.copy()
Expand All @@ -154,7 +168,12 @@ def init_user_plots():
plots = init_plots()

# Set centile types
plots['settings']['cent_types'] = ["CN", "CN-Males", "CN-Females"]
# plots['settings']['cent_types'] = ["CN", "CN-Males", "CN-Females"]
plots['settings']['cent_types'] = [
"None",
"CN-All", "CN-Males", "CN-Females",
"AD-All", "AD-Males", "AD-Females",
]

# Save in session state
st.session_state['user_plots'] = plots.copy()
Expand Down