Full conversion of MMPthal atlas to MNI152NLin6Asym space

atlases-devel/atlas-MMPthal/atlas-MMPthal_dseg.tsv

@@ -3897,46 +3897,3 @@ index	label
 13535	thal_13535
 13536	thal_13536
 13537	thal_13537
-13538	thal_13538
-13539	thal_13539
-13540	thal_13540
-13541	thal_13541
-13542	thal_13542
-13543	thal_13543
-13544	thal_13544
-13545	thal_13545
-13546	thal_13546
-13547	thal_13547
-13548	thal_13548
-13549	thal_13549
-13550	thal_13550
-13551	thal_13551
-13552	thal_13552
-13553	thal_13553
-13554	thal_13554
-13555	thal_13555
-13556	thal_13556
-13557	thal_13557
-13558	thal_13558
-13559	thal_13559
-13560	thal_13560
-13561	thal_13561
-13562	thal_13562
-13563	thal_13563
-13564	thal_13564
-13565	thal_13565
-13566	thal_13566
-13567	thal_13567
-13568	thal_13568
-13569	thal_13569
-13570	thal_13570
-13571	thal_13571
-13572	thal_13572
-13573	thal_13573
-13574	thal_13574
-13575	thal_13575
-13576	thal_13576
-13577	thal_13577
-13578	thal_13578
-13579	thal_13579
-13580	thal_13580

atlases-devel/atlas-MMPthal/get_templateflow.py

@@ -0,0 +1,8 @@
+#!/usr/bin/env python
+#
+# https://www.templateflow.org/usage/client/
+
+from templateflow import api as tflow
+path = tflow.get('MNI152NLin6Asym', desc=None, resolution=2,
+    suffix='T1w', extension='nii.gz')
+print(path)

atlases-devel/atlas-MMPthal/process_thalamus.sh

@@ -1,53 +1,42 @@
 #!/usr/bin/env bash
 
-# Start with FSL Thalamus-maxprob atlas (1mm)
-fslmaths /usr/local/fsl/data/atlases/Thalamus/Thalamus-maxprob-thr25-1mm.nii.gz -bin thalmask
-
-# Resample to match MMP atlas (1.5mm)
-#flirt \
-#    -in thalmask \
-#    -ref space-MNI152NLin2009cAsym_atlas-MMP_dseg \
-#    -usesqform \
-#    -applyxfm \
-#    -interp nearestneighbour \
-#    -out rthalmask
-
-# We have 8464 voxels in the maxprob25 thalamus mask
-#fslstats -K rthalmask rthalmask -m -v
-
-#./make_thalamus_voxels.py
+# Process atlas-MMP_space-MNI152NLin2009cAsym_res-015 to match fmriprep MNI152NLin6Asym space,
+# and add thalamus voxel ROIs
+#
+# See get_templateflow.py to get specific atlas image for grid reference
 
-#fslmaths \
-#    space-MNI152NLin2009cAsym_atlas-MMP_dseg \
-#    -add rthalatlas \
-#    space-MNI152NLin2009cAsym_atlas-MMPthal_dseg
-
-
-## Alternative approach to match templateflow 2mm atlas tpl-MNI152NLin2009cAsym_res-02_T1w.nii.gz
-## and thereby match an available fmriprep output
+# Get thalamus mask from FSL maxprob and resample to template grid
+fslmaths /usr/local/fsl/data/atlases/Thalamus/Thalamus-maxprob-thr25-1mm.nii.gz -bin thalmask
 flirt \
     -in thalmask \
-    -ref tpl-MNI152NLin2009cAsym_res-02_T1w.nii.gz \
+    -ref tpl-MNI152NLin6Asym_res-02_T1w \
     -usesqform \
     -applyxfm \
     -interp nearestneighbour \
     -out rthalmask
 
-fslstats -K rthalmask rthalmask -m -v
-
+# Make tsv labels for the MMP atlas
 ./make_MMP_tsv.py
+
+# Make thalamus voxel ROIs and add their labels to the list
 ./make_thalamus_voxels.py
 
+# Resample the source MMP atlas to desired grid
 flirt \
-    -in space-MNI152NLin2009cAsym_atlas-MMP_dseg \
-    -ref tpl-MNI152NLin2009cAsym_res-02_T1w.nii.gz \
+    -in atlas-MMP_space-MNI152NLin2009cAsym_res-015 \
+    -ref tpl-MNI152NLin6Asym_res-02_T1w \
     -usesqform \
     -applyxfm \
     -interp nearestneighbour \
-    -out space-MNI152NLin2009cAsym_res-02_atlas-MMP_dseg
+    -out atlas-MMP_space-MNI152NLin6Asym_res-02_dseg
 
+# Add the thalamus ROIs
 fslmaths \
-    space-MNI152NLin2009cAsym_res-02_atlas-MMP_dseg \
+    atlas-MMP_space-MNI152NLin6Asym_res-02_dseg \
     -add rthalatlas \
-    space-MNI152NLin2009cAsym_res-02_atlas-MMPthal_dseg
+    atlas-MMPthal_space-MNI152NLin6Asym_res-02_dseg
+
+
+
+
 

atlases/atlas-MMPthal/atlas-MMPthal_dseg.tsv

@@ -3897,46 +3897,3 @@ index	label
 13535	thal_13535
 13536	thal_13536
 13537	thal_13537
-13538	thal_13538
-13539	thal_13539
-13540	thal_13540
-13541	thal_13541
-13542	thal_13542
-13543	thal_13543
-13544	thal_13544
-13545	thal_13545
-13546	thal_13546
-13547	thal_13547
-13548	thal_13548
-13549	thal_13549
-13550	thal_13550
-13551	thal_13551
-13552	thal_13552
-13553	thal_13553
-13554	thal_13554
-13555	thal_13555
-13556	thal_13556
-13557	thal_13557
-13558	thal_13558
-13559	thal_13559
-13560	thal_13560
-13561	thal_13561
-13562	thal_13562
-13563	thal_13563
-13564	thal_13564
-13565	thal_13565
-13566	thal_13566
-13567	thal_13567
-13568	thal_13568
-13569	thal_13569
-13570	thal_13570
-13571	thal_13571
-13572	thal_13572
-13573	thal_13573
-13574	thal_13574
-13575	thal_13575
-13576	thal_13576
-13577	thal_13577
-13578	thal_13578
-13579	thal_13579
-13580	thal_13580