[Neuroimaging] Resetting gifti labeltable

[Michiel Cottaar]

Something like the following should work for that:
color_map = {0: ('red', (1., 0., 0., 1.)), 1: ('green', (0., 1., 0., 1.)), 2: ('blue', (0., 0., 1., 1.))}
This will make all the zeros in the GIFTI file to be plotted as red, all the ones as green, and all the two's as blue.

So within the loop, the variable `value` should be the integer value that you use to mark the ROI in the array. The variable `text` should be the ROI label and `rgba` should be a sequence of four numbers (red, green, blue, and alpha). You can set the alpha to zero for any labels you don't want to plot.

Good luck,

Michiel

On 26 Jul 2019, at 08:56, Emma Robinson <emma.robinson01 at gmail.com<mailto:emma.robinson01 at gmail.com>> wrote:

Thanks!

Could you possibly show me how you create your colour_map dictionary? What I've tried so far has not been working.

Emma



On Tue, 23 Jul 2019 at 13:50, Michiel Cottaar <michiel.cottaar at ndcn.ox.ac.uk<mailto:michiel.cottaar at ndcn.ox.ac.uk>> wrote:
Hi Emma,

It's a bit awkward, but the way I do this is to create an empty GiftiLabelTable and then append individual GiftiLabels to it. Note that the constructor of the GiftiLabel only expects the integer index and the RGBA colour, but you should also set a label (when serialising the GiftiLabelTable expects all labels to have such a label).

So my code looks like:

labeltable = gifti.GiftiLabelTable()
for value, (text, rgba) in color_map.items():
    labeltable.labels.append(gifti.GiftiLabel(value, *rgba))
    labeltable.labels[-1].label = str(text)

where color_map is a dictonary mapping from the indices to a tuple with the label and the RGBA value.

Cheers,

Michiel

On 23 Jul 2019, at 12:30, Emma Robinson <emma.robinson01 at gmail.com<mailto:emma.robinson01 at gmail.com>> wrote:

Hi

I am trying to create a new gifti label file using an existing one as template. How do I change the label table? I've create a new label dictionary as variable 'labeldict' but I cannot create a  GiftiLabelTable instance from this see:

nibabel.gifti.GiftiLabelTable(labeldict)
Traceback (most recent call last):

  File "<ipython-input-34-d948ed166e6e>", line 1, in <module>
    nibabel.gifti.GiftiLabelTable(labeldict)

TypeError: __init__() takes 1 positional argument but 2 were given

Could someone tell me how it is supposed to be done?

Thanks

Emma
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