Merge pull request #186 from khanlab/freesurfer-atlas

Freesurfer atlas

.github/workflows/python-testing.yml

@@ -164,6 +164,13 @@ jobs:
     - name: Test modality T1w with myelin map
       run: |
         poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T1w --generate-myelin-map
+    - name: Test modality T1w with magdeburg atlas
+      run: |
+        poetry run hippunfold test_data/bids_T1w test_out participant -np --modality T1w --atlas magdeburg
+    - name: Test modality T1w with freesurfer atlas
+      run: |
+        poetry run hippunfold test_data/bids_T1w test_out participant -np --modality T1w --atlas freesurfer
+
 
 
 

hippunfold/config/snakebids.yml

@@ -191,6 +191,7 @@ parse_args:
     choices:
       - 'bigbrain'
       - 'magdeburg'
+      - 'freesurfer'
     default: 'bigbrain'
     help: 'Select the atlas (unfolded space) to use for subfield labels. (default: %(default)s)'
 
@@ -334,6 +335,9 @@ atlas_files:
   magdeburg:
     label_nii: resources/magdeburg/sub-all_hemi-{hemi}_label-hipp_desc-manualsubfields_maxprob.nii.gz
     label_list: resources/magdeburg/magdeburg_labellist.txt
+  freesurfer:
+    label_nii: resources/freesurfer/sub-all_hemi-{hemi}_space-unfold_label-hipp_desc-freesurfersubfields_dseg.nii.gz
+    label_list: resources/freesurfer/freesurfer_labellist.txt
 
 
 rigid_reg_template: False

hippunfold/resources/freesurfer/README.md

@@ -0,0 +1,6 @@
+Freesurfer subfield atlas
+
+Generated using workflow from https://github.com/khanlab/hippunfold-create-atlas#freesurfer
+This creates probalistic and maxprob (used here) labels by running hippunfold & freesurfer subfield segmentation on ds002168 (openneuro, 48 subjects) and mapping the freesurfer labels to the unfolded space.
+
+

hippunfold/resources/freesurfer/freesurfer_labellist.txt

@@ -0,0 +1,88 @@
+alveus
+201 255 204 153 255
+perforant_pathway
+202 255 128 128 255
+parasubiculum
+203 175 175 75  255
+presubiculum
+204 64  0   64  255
+subiculum
+205 0   0   255 255
+CA1
+206 255 0   0   255
+CA2
+207 128 128 255 255
+CA3
+208 0   128 0   255
+CA4
+209 196 160 128 255
+GC-DG
+210 32  200 255 255
+HATA
+211 128 255 128 255
+fimbria
+212 204 153 204 255
+lateral_ventricle
+213 121 17  136 255
+molecular_layer_HP
+214 128 0   0   255
+hippocampal_fissure
+215 128 32  255 255
+entorhinal_cortex
+216 255 204 102 255
+molecular_layer_subiculum
+217 128 128 128 255
+Amygdala
+218 104 255 255 255
+Cerebral_White_Matter
+219 0   226 0   255
+Cerebral_Cortex
+220 205 63  78  255
+Inf_Lat_Vent
+221 197 58  250 255
+Perirhinal
+222 33  150 250 255
+Cerebral_White_Matter_Edge
+223 226 0   0   255
+Background
+224 100 100 100 255
+Ectorhinal
+225 197 150 250 255
+HP_tail
+226 170 170 255 255
+Polymorphic-Layer
+227 128 255 128 255
+Intracellular-Space
+228 204 153 204 255
+HP_body
+231 0 255 0 255
+HP_head
+232 255 0 0 255
+presubiculum-head
+233 32  0   32  255
+presubiculum-body
+234 64  0   64  255
+subiculum-head
+235 0   0   175 255
+subiculum-body
+236 0   0   255 255
+CA1-head
+237 175 75   75   255
+CA1-body
+238 255 0   0   255
+CA3-head
+239 0   80 0   255
+CA3-body
+240 0   128 0   255
+CA4-head
+241 120 90 50 255
+CA4-body
+242 196 160 128 255
+GC-ML-DG-head
+243 75   125 175 255
+GC-ML-DG-body
+244 32  200 255 255
+molecular_layer_HP-head
+245 100 25   25   255
+molecular_layer_HP-body
+246 128 0   0   255

hippunfold/resources/freesurfer/maxprob_labellist.txt

@@ -0,0 +1,88 @@
+alveus
+1 255 204 153 255
+perforant_pathway
+2 255 128 128 255
+parasubiculum
+3 175 175 75  255
+presubiculum
+4 64  0   64  255
+subiculum
+5 0   0   255 255
+CA1
+6 255 0   0   255
+CA2
+7 128 128 255 255
+CA3
+8 0   128 0   255
+CA4
+9 196 160 128 255
+GC-DG
+10 32  200 255 255
+HATA
+11 128 255 128 255
+fimbria
+12 204 153 204 255
+lateral_ventricle
+13 121 17  136 255
+molecular_layer_HP
+14 128 0   0   255
+hippocampal_fissure
+15 128 32  255 255
+entorhinal_cortex
+16 255 204 102 255
+molecular_layer_subiculum
+17 128 128 128 255
+Amygdala
+18 104 255 255 255
+Cerebral_White_Matter
+19 0   226 0   255
+Cerebral_Cortex
+20 205 63  78  255
+Inf_Lat_Vent
+21 197 58  250 255
+Perirhinal
+22 33  150 250 255
+Cerebral_White_Matter_Edge
+23 226 0   0   255
+Background
+24 100 100 100 255
+Ectorhinal
+25 197 150 250 255
+HP_tail
+26 170 170 255 255
+Polymorphic-Layer
+27 128 255 128 255
+Intracellular-Space
+28 204 153 204 255
+HP_body
+29 0 255 0 255
+HP_head
+30 255 0 0 255
+presubiculum-head
+31 32  0   32  255
+presubiculum-body
+32 64  0   64  255
+subiculum-head
+33 0   0   175 255
+subiculum-body
+34 0   0   255 255
+CA1-head
+35 175 75   75   255
+CA1-body
+36 255 0   0   255
+CA3-head
+37 0   80 0   255
+CA3-body
+38 0   128 0   255
+CA4-head
+39 120 90 50 255
+CA4-body
+40 196 160 128 255
+GC-ML-DG-head
+41 75   125 175 255
+GC-ML-DG-body
+42 32  200 255 255
+molecular_layer_HP-head
+43 100 25   25   255
+molecular_layer_HP-body
+44 128 0   0   255