[Neuroimaging] LocalGI with nipype

[Bernardoni, Fabio]

dear satra,

thanks a lot for your message. however, for me, the localGI directive does not work. basically the localGI directive (and I suspect something similar would happen to the qcache directive, which is my next step) is always changed to the autorecon2 directive, as I can see in the command.txt file or in the report.rst, or by just printing

reconall_gyri.interface.cmdline

where I have defined:


reconall_gyri = pe.Node(interface=fs.ReconAll(directive='localGI',T1_files=['/scratch/igis/data/mri/nii/64-23-371-1_atd1/20160522_121506aat1mprnssagiso60364-23-371-1atd1.nii'],ignore_exception=False, subject_id ='64-23-371-1_atd1', subjects_dir='/scratch/igis/processing/nipype/smri'), name="reconall_gyri")



so basically I think this and qcache are not yet implemented in nipype (version'0.12.0-rc1' ).

am I right or is there still something I am overlooking? how can I solve the problem?

thanks

Fabio




Dr. Fabio Bernardoni
wiss. Mitarbeiter
Psychosoziale Medizin und Entwicklungsneurowissenschaften
Tel. +49 (0)351 458-5245
Fax +49 (0)351 458-7206
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________________________________
Von: Neuroimaging [neuroimaging-bounces+fabio.bernardoni=uniklinikum-dresden.de at python.org]" im Auftrag von "Satrajit Ghosh [satra at mit.edu]
Gesendet: Freitag, 17. Juni 2016 03:25
An: Neuroimaging analysis in Python
Betreff: Re: [Neuroimaging] LocalGI with nipype

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<mailto: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<tel:%2B49%20%280%29351%20458-5245>
Fax +49 (0)351 458-7206<tel:%2B49%20%280%29351%20458-7206>
URL http://www.uniklinikum-dresden.de/psm; www.transdenlab.de<http://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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