[Neuroimaging] LocalGI with nipype

[Bernardoni, Fabio]

Dear all,

I am trying to build a nipype workflow that does a preprocessing and computes the local gyrification index (LGI) for a set of subjects.

On the freesurfer documentation I read that to compute the LGI, the pial surface must be present (very reasonable), so that one should first run recon all with the -all directive and once this has success one can run recon all with the -localGI directive:

1) recon-all -s <subj> -all
2) recon-all -s <subj> -localGI

When I implement 2) in bash I do something like:
if [ ! -f ./surf/rh.pial_lgi ]; then
	recon-all -s <subj> -localGI  2>&1

How do I implement this dependency in nipype? Normally I require that one of the output of process 1 (optimally the pial surface) is an input of process 2. But the pial surface cannot be an input of process 2 because the ReconAll node does not accept the pial surface as input (there is in general no output of ReconAll that is also its input). So, is the solution to create a derived class ReconAll_LGI with these properties?

Thanks
Fabio



Dr. Fabio Bernardoni
wiss. Mitarbeiter
Psychosoziale Medizin und Entwicklungsneurowissenschaften
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