Seed-based connectivity

Seed-based connectivity provides the opportunity to compute the functional connectivity between the a point/region and all other voxels in the brain. The users can specify a 3 coordinates point in mm of a template or a mask with the same dimension and orietation of a template. If no template is provided, MNI152_T1_2mm_brain.nii.gz will be used as default template.

The seed connectivity is done with ${XCPEDIR}/utils/seedconnectivity:

${XCPEDIR}/utils/seedconnectivity   \
-i  input4Dimage  \     #  4D inputimage usually residualised or image or filtered image
-s  x,y,z   \           # 3 cordinates  or a mask (--s=/path/to/mask)
-o  outputpath  \       # output directory
-r  radius \            # radius of the mask for 3 points cordinates, r=5 is default
-k  kernel \            # kernel size if the image is not filtered
-t  template  \         # template; MNI152_T1_2mm_brain.nii.gz is default
-n  seed_name \         # SEED will used as default
-p  subject identifiers

The first three opions (-img,–sand -o ) are mandatory. If the input image is residualised BOLD image (regress/sub-*residualized.nii.gz) from regress module which is not spatially smooth, theuser is encourage to smooth the image. Kernel of 5mm FHWM is preffered for good connectivity results.

Expected outputs A sub-directory of seed_names is created in seed directory. The directory constist of:

-prefix_connectivity_{seed_name}_seed.nii.gz # seed mask in BOLD space
-prefix_connectivity_{seed_name}_smK.nii.gz # seed correlation map, K is kernel size
-prefix_connectivity_{seed_name}Z_smK.nii.gz # Fisherz transfromed seed correlation map
-prefix_connectivity_{seed_name}_ts.1D # time series of seed point/mask