TANS

.gitmodules

@@ -1,3 +1,6 @@
 [submodule "contarg/test/data"]
 	path = contarg/test/data
 	url = https://github.com/nih-fmrif/contarg_test_data.git
+[submodule "contarg/resources/Targeted-Functional-Network-Stimulation"]
+	path = contarg/resources/Targeted-Functional-Network-Stimulation
+	url = https://github.com/Shotgunosine/Targeted-Functional-Network-Stimulation

README.md

@@ -42,29 +42,42 @@ contarg hierarchical run \
 * Seedmap + classic
     *   `contarg seedmap run --targeting-method=classic`
 * Seedmap + cluster
-    *   `contarg seedmap run --targeting-method=cluster`  
+    *   `contarg seedmap run --targeting-method=cluster`
+* TANS + refernce correlation
+    *   `contarg tans run --target-method=reference`
+* TANS + depression circuit spatial similarity 
+    *   `contarg tans run --target-method=DCSS`
 
 For Seedmap methods you should provide a seedmap in MIN152NLin6Asym space.
 You can use the one in test/data/derivatives/contarg/seedmap/hcp_working, 
 remember you may need to download it with `datalad get`. 
 Alternatively, you can use `contarg seedmap subjectmap` and `contarg seedmap groupmap` to make one.
 
+TANS is Targeted Functional Network Stimulation implemented by Chuck Lynch. I've just wrapped it in python and made a 
+CLI. In order to run that, you will need Matlab, Freesurfer, FSL, connectome-workbench, ANTs, and SimNibs 4.0.
+
 ## ROIs
-Currently we just have spherical ROIs based on Cash et al., 2022 for defining SGC and DLPFC.
-They were created as follows.
+We've vot 4 reference masks and 4 stim masks. Most were created via the AFNI commands below. coleBA46 was based on extraction of MNI 
+coordinates from Cole et al., 2020. We hand traced an ROI that enclosed those points and followed gyral landmarks on 
+MNI152NLin6Asym (1mm resolution). We then cleaned up the hand traced mask via inlation/delation and fit it with a convex
+hull using Mango. 
 ```commandline
-# make SGC mask
+# make SGC mask 10 mm sphere at MNI 6,16,-10
 3dcalc -a ~/.cache/templateflow/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz   \
        -expr 'step(100-(x+6)*(x+6)-(y+16)*(y+16)-(z+10)*(z+10))' \
        -prefix SGCsphere_space-MNI152NLin6Asym_res-02.nii.gz
-# make blSGC mask
+# make blSGC mask 10 mm spheres at (-6,16,-10 and 6,16,-10)
 3dcalc -a ~/.cache/templateflow/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz   \
        -expr 'step(100-(x-6)*(x-6)-(y+16)*(y+16)-(z+10)*(z+10))' \
        -prefix leftSGCsphere_space-MNI152NLin6Asym_res-02.nii.gz
 3dcalc -a SGCsphere_space-MNI152NLin6Asym_res-02.nii.gz   \
        -b leftSGCsphere_space-MNI152NLin6Asym_res-02.nii.gz    \
        -expr 'step(a+b)' \
        -prefix bilateralSGCspheres_space-MNI152NLin6Asym_res-02.nii.gz
+# make a bilateral full SGC mask 12 mm sphere at 0, 24, -14
+3dcalc -a ~/.cache/templateflow/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz   \
+       -expr 'step(144-(x-0)*(x-0)-(y+24)*(y+24)-(z+14)*(z+14))' \
+       -prefix bilateralfullSGCsphere_space-MNI152NLin6Asym_res-02.nii.gz
 # BA9 20mm -36, 39, 43
 3dcalc -a ~/.cache/templateflow/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz   \
        -expr 'step(400-(x-36)*(x-36)-(y+39)*(y+39)-(z-43)*(z-43))' \
@@ -84,12 +97,38 @@ They were created as follows.
 3dcalc -a ~/.cache/templateflow/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz   \
        -expr 'step(400-(x-37)*(x-37)-(y+26)*(y+26)-(z-49)*(z-49))' \
        -prefix F3sphere_space-MNI152NLin6Asym_res-02.nii.gz
+
+# BA9 30mm -36, 39, 43
+3dcalc -a ~/.cache/templateflow/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz   \
+       -expr 'step(900-(x-36)*(x-36)-(y+39)*(y+39)-(z-43)*(z-43))' \
+       -prefix dilatedBA9sphere_space-MNI152NLin6Asym_res-02.nii.gz
+
+# BA46 30mm -44, 40, 29
+3dcalc -a ~/.cache/templateflow/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz   \
+       -expr 'step(900-(x-44)*(x-44)-(y+40)*(y+40)-(z-29)*(z-29))' \
+       -prefix dilatedBA46sphere_space-MNI152NLin6Asym_res-02.nii.gz
+
+# 5cm 30mm -41, 16, 54
+3dcalc -a ~/.cache/templateflow/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz   \
+       -expr 'step(900-(x-41)*(x-41)-(y+16)*(y+16)-(z-54)*(z-54))' \
+       -prefix dilated5cmsphere_space-MNI152NLin6Asym_res-02.nii.gz
+
+# F3 30mm -37, 26, 49
+3dcalc -a ~/.cache/templateflow/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz   \
+       -expr 'step(900-(x-37)*(x-37)-(y+26)*(y+26)-(z-49)*(z-49))' \
+       -prefix dilatedF3sphere_space-MNI152NLin6Asym_res-02.nii.gz
 
 # DLPFC
 3dcalc -a BA9sphere_space-MNI152NLin6Asym_res-02.nii.gz -b BA46sphere_space-MNI152NLin6Asym_res-02.nii.gz \
        -c 5cmsphere_space-MNI152NLin6Asym_res-02.nii.gz -d F3sphere_space-MNI152NLin6Asym_res-02.nii.gz  \
        -expr 'step(a + b + c + d)'  \
        -prefix DLPFCspheres_space-MNI152NLin6Asym_res-02.nii.gz
+
+# Dilated DLPFC
+3dcalc -a dilatedBA9sphere_space-MNI152NLin6Asym_res-02.nii.gz -b dilatedBA46sphere_space-MNI152NLin6Asym_res-02.nii.gz \
+       -c dilated5cmsphere_space-MNI152NLin6Asym_res-02.nii.gz -d dilatedF3sphere_space-MNI152NLin6Asym_res-02.nii.gz  \
+       -expr 'step(a + b + c + d)'  \
+       -prefix dilatedDLPFCspheres_space-MNI152NLin6Asym_res-02.nii.gz
 
 # DLPFC + brainmask
 3dcalc -a BA9sphere_space-MNI152NLin6Asym_res-02.nii.gz -b BA46sphere_space-MNI152NLin6Asym_res-02.nii.gz \

contarg/cli/cli.py

@@ -1,8 +1,11 @@
 import click
 from .run_hierarchical import contarg
 from .run_seedmap import contarg as contargsm
+from .run_tans import contarg as contargtans
+from .run_pfm import contarg as contargpfm
 
-contarg = click.CommandCollection(sources=[contarg, contargsm])
+
+contarg = click.CommandCollection(sources=[contarg, contargsm, contargtans, contargpfm])
 
 if __name__ == "__main__":
     contarg()