ConTarg
A python package implementing/wrapping methods for functional connectivity personalized targeting of rTMS therapy.
Getting test data
git submodule init
git submodule update
datalad get contarg/test/data/derivatives/fmriprep/sub-*/anat/sub-*_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5 \
contarg/test/data/derivatives/fmriprep/sub-*/anat/*preproc_T1w.* \
contarg/test/data/derivatives/fmriprep/sub-*/func/*preproc_bold.* \
contarg/test/data/derivatives/fmriprep/sub-*/func/*brain_mask.* \
contarg/test/data/derivatives/fmriprep/sub-*/func/*boldref.* \
contarg/test/data/derivatives/fmriprep/sub-*/func/*confounds_timeseries.* \
contarg/test/data/derivatives/contarg/hierarchical/testing*_ref \
contarg/test/data/derivatives/contarg/hierarchical/testing1sub/**/*mask.nii.gz \
contarg/test/data/derivatives/contarg/hierarchical/testing2subs/**/*mask.nii.gz
Example run
contarg hierarchical run \
--bids-dir=data/ds002330 \
--derivatives-dir=data/derivatives/ \
--database-file=data/pybids_0.15.2_db \
--run-name=firsttest \
--space=T1w \
--smoothing-fwhm=3 \
--ndummy=5 \
--tr=1.9 \
--subject=02 \
--run=1 \
--njobs=2
Implemented methods
- Hierarchical clustering
contarg hierarchical run
- Seedmap + classic
contarg seedmap run --targeting-method=classic
- Seedmap + cluster
contarg seedmap run --targeting-method=cluster
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.
ROIs
Currently we just have spherical ROIs based on Cash et al., 2022 for defining SGC and DLPFC. They were created as follows.
# make SGC mask
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
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
# 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))' \
-prefix BA9sphere_space-MNI152NLin6Asym_res-02.nii.gz
# BA46 20mm -44, 40, 29
3dcalc -a ~/.cache/templateflow/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz \
-expr 'step(400-(x-44)*(x-44)-(y+40)*(y+40)-(z-29)*(z-29))' \
-prefix BA46sphere_space-MNI152NLin6Asym_res-02.nii.gz
# 5cm 20mm -41, 16, 54
3dcalc -a ~/.cache/templateflow/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz \
-expr 'step(400-(x-41)*(x-41)-(y+16)*(y+16)-(z-54)*(z-54))' \
-prefix 5cmsphere_space-MNI152NLin6Asym_res-02.nii.gz
# F3 20mm -37, 26, 49
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
# 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
# DLPFC + brainmask
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 \
-e ~/.cache/templateflow/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_desc-brain_T1w.nii.gz \
-expr 'and(step(a + b + c + d),e)' \
-prefix DLPFCspheresmasked_space-MNI152NLin6Asym_res-02.nii.gz
# BA46 + brainmask
3dcalc -a /usr/local/apps/fsl/6.0.4/data/standard/MNI152_T1_2mm.nii.gz \
-b ~/.cache/templateflow/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_desc-brain_T1w.nii.gz \
-expr 'and(a,b)' \
-prefix BA46spheremasked_space-MNI152NLin6Asym_res-02.nii.gz
This is a Python project packaged according to Contemporary Python Packaging - 2023.
