<div dir="ltr">So, now all the code seems to work except for the plotting, still.<div>A very python beginner question: How can I store the coordinates + the corresponding accuracies? (e.g. in Matlab that could be done quite easily with the ''save'' command).<br><div><br></div><div>Regarding plotting: I stored the outputed nifti, and of course I can open it in MRIcron etc., but I'd prefer to be able to plot the results in a way where the distribution of accuracies over space is visible (as in the plotting example).</div><div><br></div><div>So, how comes the plotting still is so not-sensible?</div><div><br></div><div>Here code & attached again how the plot looks like, sorry for all the questions!:-)</div><div><br></div><div><div># plotting</div><div><br></div><div>plot_args = {</div><div> 'background' : 'Struct.nii',</div><div> 'background_mask' : 'brain.nii',</div><div> 'overlay_mask' : 'S1_mask.nii',</div><div> 'do_stretch_colors' : False,</div><div> 'cmap_bg' : 'gray',</div><div> 'cmap_overlay' : 'autumn', # YlOrRd_r # pl.cm.autumn</div><div> 'interactive' : cfg.getboolean('examples', 'interactive', True)</div><div>}</div><div><br></div><div>fig = pl.figure(figsize=(12, 4), facecolor='white')</div><div><br></div><div>subfig = plot_lightbox(</div><div> overlay=niftiresults,</div><div> vlim=(0.5, None), slices=range(23,31),</div><div> fig=fig, </div><div> background='Struct.nii',</div><div> background_mask='brain.nii',</div><div> overlay_mask='S1_mask.nii',</div><div> **plot_args</div><div>)</div><div><br></div><div>pl.title('Accuracy distribution for radius %i' % radius_)</div><div><br></div><div>pl.show()</div><div>pl.savefig('plotResults')</div></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Sep 13, 2017 at 12:07 AM, Yaroslav Halchenko <span dir="ltr"><<a href="mailto:yoh@onerussian.com" target="_blank">yoh@onerussian.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class=""><br>
On Tue, 12 Sep 2017, Pegah Kassraian Fard wrote:<br>
<br>
</span><span class="">> I would out-comment the line I would not need..so I do use the maximal<br>
> accuracy.<br>
> Attached is a plot..<br>
<br>
</span>try to plot just a few slices<br>
<br>
or ideally just open that produced .nii.gz in any application you<br>
typically use for your visualization (FSLeyes, AFNI, whatnot)<br>
<span class=""><br>
> Many thanks<br>
> On Tue, Sep 12, 2017 at 10:19 PM, Yaroslav Halchenko <<a href="mailto:yoh@onerussian.com">yoh@onerussian.com</a>><br>
> wrote:<br>
<br>
> On Tue, 12 Sep 2017, Pegah Kassraian Fard wrote:<br>
<br>
</span>> >Â Â yes yes, when I ran the code I switch between these...so that<br>
> was/is a<br>
> >Â Â residuum of how I did it so far:)<br>
<span class=""><br>
> so your extremum is the minimal accuracy... how useful is that ;)?<br>
</span>> >Â Â Â > now. I am yet classifying whole brain, just as a check.<br>
> >Â Â Â > Also,Ã*Â the plotting seems completely off...and the output<br>
<span class="">> either<br>
<br>
> what is "off" here? screenshot?<br>
</span>> >Â Â Â > non-existent or really weird. Is there any chance anyone<br>
> could quickly<br>
> >Â Â Â run<br>
> >Â Â Â > the code? Or would you have any other suggestions?<br>
<div class="HOEnZb"><div class="h5"><br>
> might try later<br>
<br>
> cheers,<br>
--<br>
Yaroslav O. Halchenko<br>
Center for Open Neuroscience <a href="http://centerforopenneuroscience.org" rel="noreferrer" target="_blank">http://<wbr>centerforopenneuroscience.org</a><br>
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755<br>
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WWW: <a href="http://www.linkedin.com/in/yarik" rel="noreferrer" target="_blank">http://www.linkedin.com/in/<wbr>yarik</a><br>
</div></div></blockquote></div><br></div>