<div dir="ltr">hi fabio,<div><br></div><div>could you please open an issue on github? we can continue this discussion there.</div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr">cheers,<br><br>satra<br><br></div></div></div><div class="gmail_quote">On Fri, Jun 17, 2016 at 7:41 AM, Bernardoni, Fabio <span dir="ltr"><<a href="mailto:Fabio.Bernardoni@uniklinikum-dresden.de" target="_blank">Fabio.Bernardoni@uniklinikum-dresden.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt">dear satra,<br>
<br>
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
<p style="margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;text-indent:0px">
reconall_gyri.interface.cmdline</p>
<p style="margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;text-indent:0px">
where I have defined:</p>
<br>
<p style="margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;text-indent:0px">
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")</p>
<p style="margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;text-indent:0px">
<br>
</p>
<p style="margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;text-indent:0px">
<br>
</p>
<p style="margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;text-indent:0px">
so basically I think this and qcache are not yet implemented in nipype (version'0.12.0-rc1' ).
<br>
</p>
<br>
am I right or is there still something I am overlooking? how can I solve the problem?<br>
<br>
thanks<span class=""><br>
<br>
Fabio<br>
<br>
<br>
<div><br>
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<p><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">Dr. Fabio Bernardoni<br>
</span></p>
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<div style="direction:ltr"><font face="Tahoma" color="#000000" size="2"><b>Von:</b> Neuroimaging [neuroimaging-bounces+fabio.bernardoni=<a href="mailto:uniklinikum-dresden.de@python.org" target="_blank">uniklinikum-dresden.de@python.org</a>]" im Auftrag von "Satrajit Ghosh [<a href="mailto:satra@mit.edu" target="_blank">satra@mit.edu</a>]<br>
<b>Gesendet:</b> Freitag, 17. Juni 2016 03:25<br>
<b>An:</b> Neuroimaging analysis in Python<br>
<b>Betreff:</b> Re: [Neuroimaging] LocalGI with nipype<br>
</font><br>
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<div dir="ltr">dear fabio,
<div><br>
</div>
<div>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.</div>
<div class="gmail_extra"><br clear="all">
<div>
<div>
<div dir="ltr">cheers,<br>
<br>
satra<br>
<br>
</div>
</div>
</div>
<div class="gmail_quote">On Wed, Jun 15, 2016 at 1:51 PM, Bernardoni, Fabio <span dir="ltr">
<<a href="mailto:Fabio.Bernardoni@uniklinikum-dresden.de" target="_blank">Fabio.Bernardoni@uniklinikum-dresden.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear all,<br>
<br>
I am trying to build a nipype workflow that does a preprocessing and computes the local gyrification index (LGI) for a set of subjects.<br>
<br>
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:<br>
<br>
1) recon-all -s <subj> -all<br>
2) recon-all -s <subj> -localGI<br>
<br>
When I implement 2) in bash I do something like:<br>
if [ ! -f ./surf/rh.pial_lgi ]; then<br>
recon-all -s <subj> -localGI 2>&1<br>
<br>
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?<br>
<br>
Thanks<br>
Fabio<br>
<br>
<br>
<br>
Dr. Fabio Bernardoni<br>
wiss. Mitarbeiter<br>
Psychosoziale Medizin und Entwicklungsneurowissenschaften<br>
Tel. <a href="tel:%2B49%20%280%29351%20458-5245" value="+493514585245" target="_blank">
+49 (0)351 458-5245</a><br>
Fax <a href="tel:%2B49%20%280%29351%20458-7206" value="+493514587206" target="_blank">
+49 (0)351 458-7206</a><br>
URL <a href="http://www.uniklinikum-dresden.de/psm" rel="noreferrer" target="_blank">
http://www.uniklinikum-dresden.de/psm</a>; <a href="http://www.transdenlab.de" rel="noreferrer" target="_blank">
www.transdenlab.de</a><br>
Universitätsklinikum Carl Gustav Carus & Medizinische Fakultät<br>
an der Technischen Universität Dresden<br>
Anstalt des öffentlichen Rechts des Freistaates Sachsen<br>
Fetscherstraße 74, 01307 Dresden<br>
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