4. Measuring regional brain volumes¶
Contents
Sammba-MRI allows to measure regional brain volumes in regions outlined in an atlas. This can be useful to measure cerebral atrophy for example.
4.1. Step 1 - Registering several MRI images to an existing template¶
Sammba-MRI allows to register several MR images to an existing template.
The function to use is > anats_to_template(images_to_register, Template_name, Saved_Registered_dir, 400, caching=False)
4.2. Step 2 - Align the Atlas on the raw MR images thanks to the deformation evaluated in step 1¶
So far we did not develop any Sammba procedure to perform this task We recommend to use the > 3dNwarpApply funtion from AFNI:
3dNwarpApply -nwarp Saved_Registered_dir/Aal1_WARP.nii.gz Saved_Registered_dir/
Aal1_masked_shr.aff12.1D -iwarp -source Atlas_Directory/Atlas.nii.gz -master
Images-to-Register/Aal1.nii.gz -ainterp NN -prefix Measures/Aal1_atlas.nii.gz
4.3. Step 3 - Measure of the volume of each registered ROI of the atlas¶
So far we did not develop any Sammba procedure to perform this task We recommend to use the > 3dhistog from AFNI:
3dhistog -int Measures/Aal1_atlas.nii.gz > Measures/Aal1-Measured-volumes.txt