So, now all the code seems to work except for the plotting, still. 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).
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). So, how comes the plotting still is so not-sensible? Here code & attached again how the plot looks like, sorry for all the questions!:-) # plotting plot_args = { 'background' : 'Struct.nii', 'background_mask' : 'brain.nii', 'overlay_mask' : 'S1_mask.nii', 'do_stretch_colors' : False, 'cmap_bg' : 'gray', 'cmap_overlay' : 'autumn', # YlOrRd_r # pl.cm.autumn 'interactive' : cfg.getboolean('examples', 'interactive', True) } fig = pl.figure(figsize=(12, 4), facecolor='white') subfig = plot_lightbox( overlay=niftiresults, vlim=(0.5, None), slices=range(23,31), fig=fig, background='Struct.nii', background_mask='brain.nii', overlay_mask='S1_mask.nii', **plot_args ) pl.title('Accuracy distribution for radius %i' % radius_) pl.show() pl.savefig('plotResults') On Wed, Sep 13, 2017 at 12:07 AM, Yaroslav Halchenko <y...@onerussian.com> wrote: > > On Tue, 12 Sep 2017, Pegah Kassraian Fard wrote: > > > I would out-comment the line I would not need..so I do use the maximal > > accuracy. > > Attached is a plot.. > > try to plot just a few slices > > or ideally just open that produced .nii.gz in any application you > typically use for your visualization (FSLeyes, AFNI, whatnot) > > > Many thanks > > On Tue, Sep 12, 2017 at 10:19 PM, Yaroslav Halchenko < > y...@onerussian.com> > > wrote: > > > On Tue, 12 Sep 2017, Pegah Kassraian Fard wrote: > > > >Â Â yes yes, when I ran the code I switch between these...so that > > was/is a > > >Â Â residuum of how I did it so far:) > > > so your extremum is the minimal accuracy... how useful is that ;)? > > >Â Â Â > now. I am yet classifying whole brain, just as a check. > > >Â Â Â > Also,Ã*Â the plotting seems completely off...and the > output > > either > > > what is "off" here? screenshot? > > >Â Â Â > non-existent or really weird. Is there any chance anyone > > could quickly > > >Â Â Â run > > >Â Â Â > the code? Or would you have any other suggestions? > > > might try later > > > cheers, > -- > Yaroslav O. Halchenko > Center for Open Neuroscience http://centerforopenneuroscience.org > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 > WWW: http://www.linkedin.com/in/yarik >
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