[Neuroimaging] LocalGI with nipype

[Satrajit Ghosh]

dear fabio,

recon-all provides subject_id as an output. so you can send that to a
second recon-all (named differently that then computes the localGI.

cheers,

satra

On Wed, Jun 15, 2016 at 1:51 PM, Bernardoni, Fabio <
Fabio.Bernardoni at uniklinikum-dresden.de> wrote:

> 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
> Tel. +49 (0)351 458-5245
> Fax +49 (0)351 458-7206
> URL http://www.uniklinikum-dresden.de/psm; www.transdenlab.de
> Universitätsklinikum Carl Gustav Carus & Medizinische Fakultät
> an der Technischen Universität Dresden
> Anstalt des öffentlichen Rechts des Freistaates Sachsen
> Fetscherstraße 74, 01307 Dresden
> http://www.uniklinikum-dresden.de
> Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
> Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba
> USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
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