[Neuroimaging] LocalGI with nipype

[Satrajit Ghosh]

hi fabio,

could you please open an issue on github? we can continue this discussion
there.

cheers,

satra

On Fri, Jun 17, 2016 at 7:41 AM, Bernardoni, Fabio <
Fabio.Bernardoni at uniklinikum-dresden.de> wrote:

> 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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> www.transdenlab.de
> <https://owa.uniklinikum-dresden.de/owa/redir.aspx?REF=tQAdr-khC1WP3CMvWfhsoAKiSVCgAjPGenEqKlUQx0WNjlN-UonTCAFodHRwOi8vd3d3LnRyYW5zZGVubGFiLmRlLw..>
>
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> an der Technischen Universität Dresden
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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> 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
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
>
>
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