help > Color Bar Limits - Connectivity RIng scaling;
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Jul 11, 2020 08:07 AM | Paul Summers
Color Bar Limits - Connectivity RIng scaling;
Hi,
In Results Explorer, after 2nd level processing:
It appears that the colours applied to the connections are based on the range: 0 - Max score for each individual seed ROI
The colour bar in the top right of the display, on the other hand uses the Max score across all seed ROIs.
This creates an erroneous impression of statistical strength both:
- when looking at the full set of connections, far too many appear to have high scores. In the top panel of the figure,attached, quite a few connections display as red-brown, despite there being only a handful of connections with a statistic above 200; so by the color scale above, almost all the connections should be yellowish;
and:
- when looking at connections for just one ROI (bottom panel of figure attached) as we can see in the table below that the maximum statistic is 72, but the colorbar still ranges to 813. Nonetheless, the colors of the connections use the full colorscale. If one doesn't loo
I believe most readers will misinterpret the figure in both contexts as they will expect the colours to scale linearly across the colorbar range not
across the individual ROI statistics range that needs to be dug out to the table below the figure.
As well as scaling to the range displayed in the colour bar, as mentioned by another user just a day or so ago, if one is creating separate displays of connections for individual ROIs it would be nice to be able to force the limits of the colorbar to remain the same across each display by inserting a parameter somewhere. Maybe this is under Graphics Options, but the functionality tied to the button appears to be inactive (Conn19.c on Matlab 2019a).
Thanks
Paul S
In Results Explorer, after 2nd level processing:
It appears that the colours applied to the connections are based on the range: 0 - Max score for each individual seed ROI
The colour bar in the top right of the display, on the other hand uses the Max score across all seed ROIs.
This creates an erroneous impression of statistical strength both:
- when looking at the full set of connections, far too many appear to have high scores. In the top panel of the figure,attached, quite a few connections display as red-brown, despite there being only a handful of connections with a statistic above 200; so by the color scale above, almost all the connections should be yellowish;
and:
- when looking at connections for just one ROI (bottom panel of figure attached) as we can see in the table below that the maximum statistic is 72, but the colorbar still ranges to 813. Nonetheless, the colors of the connections use the full colorscale. If one doesn't loo
I believe most readers will misinterpret the figure in both contexts as they will expect the colours to scale linearly across the colorbar range not
across the individual ROI statistics range that needs to be dug out to the table below the figure.
As well as scaling to the range displayed in the colour bar, as mentioned by another user just a day or so ago, if one is creating separate displays of connections for individual ROIs it would be nice to be able to force the limits of the colorbar to remain the same across each display by inserting a parameter somewhere. Maybe this is under Graphics Options, but the functionality tied to the button appears to be inactive (Conn19.c on Matlab 2019a).
Thanks
Paul S
Jul 11, 2020 01:07 PM | Alfonso Nieto-Castanon - Boston University
RE: Color Bar Limits - Connectivity RIng scaling;
Hi Paul,
Thank you very much for the detailed report, it definitely helps. I am attaching a patch to fix this scaling issue (this patch is for release 19c, to install it simply copy the attached file to your conn distribution folder overwriting the file with the same name there; the same patch has been added to the current development version).
Please let me know if you still run into any issues. I have also tentatively added in the patch the option to click on the colorbar to more easily change the colorbar limits (you may also do that programmatically using, for example, the syntax "conn_display(gcf, 'display.colorbar.limit', 10)" -either clicking on the figure first or changing gcf to the results explorer figure handle-).
Best
Alfonso
Originally posted by Paul Summers:
Thank you very much for the detailed report, it definitely helps. I am attaching a patch to fix this scaling issue (this patch is for release 19c, to install it simply copy the attached file to your conn distribution folder overwriting the file with the same name there; the same patch has been added to the current development version).
Please let me know if you still run into any issues. I have also tentatively added in the patch the option to click on the colorbar to more easily change the colorbar limits (you may also do that programmatically using, for example, the syntax "conn_display(gcf, 'display.colorbar.limit', 10)" -either clicking on the figure first or changing gcf to the results explorer figure handle-).
Best
Alfonso
Originally posted by Paul Summers:
Hi,
In Results Explorer, after 2nd level processing:
It appears that the colours applied to the connections are based on the range: 0 - Max score for each individual seed ROI
The colour bar in the top right of the display, on the other hand uses the Max score across all seed ROIs.
This creates an erroneous impression of statistical strength both:
- when looking at the full set of connections, far too many appear to have high scores. In the top panel of the figure,attached, quite a few connections display as red-brown, despite there being only a handful of connections with a statistic above 200; so by the color scale above, almost all the connections should be yellowish;
and:
- when looking at connections for just one ROI (bottom panel of figure attached) as we can see in the table below that the maximum statistic is 72, but the colorbar still ranges to 813. Nonetheless, the colors of the connections use the full colorscale. If one doesn't loo
I believe most readers will misinterpret the figure in both contexts as they will expect the colours to scale linearly across the colorbar range not
across the individual ROI statistics range that needs to be dug out to the table below the figure.
As well as scaling to the range displayed in the colour bar, as mentioned by another user just a day or so ago, if one is creating separate displays of connections for individual ROIs it would be nice to be able to force the limits of the colorbar to remain the same across each display by inserting a parameter somewhere. Maybe this is under Graphics Options, but the functionality tied to the button appears to be inactive (Conn19.c on Matlab 2019a).
Thanks
Paul S
In Results Explorer, after 2nd level processing:
It appears that the colours applied to the connections are based on the range: 0 - Max score for each individual seed ROI
The colour bar in the top right of the display, on the other hand uses the Max score across all seed ROIs.
This creates an erroneous impression of statistical strength both:
- when looking at the full set of connections, far too many appear to have high scores. In the top panel of the figure,attached, quite a few connections display as red-brown, despite there being only a handful of connections with a statistic above 200; so by the color scale above, almost all the connections should be yellowish;
and:
- when looking at connections for just one ROI (bottom panel of figure attached) as we can see in the table below that the maximum statistic is 72, but the colorbar still ranges to 813. Nonetheless, the colors of the connections use the full colorscale. If one doesn't loo
I believe most readers will misinterpret the figure in both contexts as they will expect the colours to scale linearly across the colorbar range not
across the individual ROI statistics range that needs to be dug out to the table below the figure.
As well as scaling to the range displayed in the colour bar, as mentioned by another user just a day or so ago, if one is creating separate displays of connections for individual ROIs it would be nice to be able to force the limits of the colorbar to remain the same across each display by inserting a parameter somewhere. Maybe this is under Graphics Options, but the functionality tied to the button appears to be inactive (Conn19.c on Matlab 2019a).
Thanks
Paul S
Jul 19, 2020 01:07 PM | Paul Summers
RE: Color Bar Limits - Connectivity RIng scaling;
Hi Alfonso,
thank-you for the patch, it works for changing the number attached to the color bar. but it does not seem to alter the connection colors in the figure
to correspond to the limits set in the colorbar. This is perhaps even more dangerous than the situation before - because the limit stays fixed when choosing a new connection or cluster to examine - putting them on a scale that doesn't correspond to that which is shown (a bit like the default display of all connections where the maximum of all connections is indicated in the colorbar, but each cluster is scaled according to its own maximum).
It seems that the value set for the colorbar needs to be passed into the display routine to ensure the connection colors are then scaled according to the indicated color scale. I couldn't figure out where or how in the code though (I did note a curiosity n a facecolor assignment (line 2900 in my copy: facecolor = 0*(.1+.8*data.plotconnoptions.BCOLOR) + 1*round(1-data.plotconnoptions.BCOLOR);
don't the 0* and 1* reduce this assignment to: facecolor = round(1-data.plotconnoptions.BCOLOR); ?
I believe the new question: " ROI-to-ROI analysis: set scaling for the colours " on jul 16 by Nathalie Rieser touches on the same issue about scaling.
Paul
thank-you for the patch, it works for changing the number attached to the color bar. but it does not seem to alter the connection colors in the figure
to correspond to the limits set in the colorbar. This is perhaps even more dangerous than the situation before - because the limit stays fixed when choosing a new connection or cluster to examine - putting them on a scale that doesn't correspond to that which is shown (a bit like the default display of all connections where the maximum of all connections is indicated in the colorbar, but each cluster is scaled according to its own maximum).
It seems that the value set for the colorbar needs to be passed into the display routine to ensure the connection colors are then scaled according to the indicated color scale. I couldn't figure out where or how in the code though (I did note a curiosity n a facecolor assignment (line 2900 in my copy: facecolor = 0*(.1+.8*data.plotconnoptions.BCOLOR) + 1*round(1-data.plotconnoptions.BCOLOR);
don't the 0* and 1* reduce this assignment to: facecolor = round(1-data.plotconnoptions.BCOLOR); ?
I believe the new question: " ROI-to-ROI analysis: set scaling for the colours " on jul 16 by Nathalie Rieser touches on the same issue about scaling.
Paul
Jul 19, 2020 11:07 PM | Alfonso Nieto-Castanon - Boston University
RE: Color Bar Limits - Connectivity RIng scaling;
Hi Paul,
Sorry about that, could you please try the attached up-to-date version directly and let me know if you are still running into any issues? (this patch is for release 19c, to install it unzip this file and copy all of its contents to your conn distribution folder overwriting the files with the same name there)
Best
Alfonso
Originally posted by Paul Summers:
Sorry about that, could you please try the attached up-to-date version directly and let me know if you are still running into any issues? (this patch is for release 19c, to install it unzip this file and copy all of its contents to your conn distribution folder overwriting the files with the same name there)
Best
Alfonso
Originally posted by Paul Summers:
Hi Alfonso,
thank-you for the patch, it works for changing the number attached to the color bar. but it does not seem to alter the connection colors in the figure
to correspond to the limits set in the colorbar. This is perhaps even more dangerous than the situation before - because the limit stays fixed when choosing a new connection or cluster to examine - putting them on a scale that doesn't correspond to that which is shown (a bit like the default display of all connections where the maximum of all connections is indicated in the colorbar, but each cluster is scaled according to its own maximum).
It seems that the value set for the colorbar needs to be passed into the display routine to ensure the connection colors are then scaled according to the indicated color scale. I couldn't figure out where or how in the code though (I did note a curiosity n a facecolor assignment (line 2900 in my copy: facecolor = 0*(.1+.8*data.plotconnoptions.BCOLOR) + 1*round(1-data.plotconnoptions.BCOLOR);
don't the 0* and 1* reduce this assignment to: facecolor = round(1-data.plotconnoptions.BCOLOR); ?
I believe the new question: " ROI-to-ROI analysis: set scaling for the colours " on jul 16 by Nathalie Rieser touches on the same issue about scaling.
Paul
thank-you for the patch, it works for changing the number attached to the color bar. but it does not seem to alter the connection colors in the figure
to correspond to the limits set in the colorbar. This is perhaps even more dangerous than the situation before - because the limit stays fixed when choosing a new connection or cluster to examine - putting them on a scale that doesn't correspond to that which is shown (a bit like the default display of all connections where the maximum of all connections is indicated in the colorbar, but each cluster is scaled according to its own maximum).
It seems that the value set for the colorbar needs to be passed into the display routine to ensure the connection colors are then scaled according to the indicated color scale. I couldn't figure out where or how in the code though (I did note a curiosity n a facecolor assignment (line 2900 in my copy: facecolor = 0*(.1+.8*data.plotconnoptions.BCOLOR) + 1*round(1-data.plotconnoptions.BCOLOR);
don't the 0* and 1* reduce this assignment to: facecolor = round(1-data.plotconnoptions.BCOLOR); ?
I believe the new question: " ROI-to-ROI analysis: set scaling for the colours " on jul 16 by Nathalie Rieser touches on the same issue about scaling.
Paul
Aug 3, 2020 10:08 AM | Paul Summers
RE: Color Bar Limits - Connectivity RIng scaling;
Hi Alfonso,
It seems to me that the patch of 20200720 is indeed working to colorize the connectome ring in the manner I would consider correct.
Thanks for the intervention!
Paul
Hi Paul,
Sorry about that, could you please try the attached up-to-date version directly and let me know if you are still running into any issues? (this patch is for release 19c, to install it unzip this file and copy all of its contents to your conn distribution folder overwriting the files with the same name there)
Best
Alfonso
It seems to me that the patch of 20200720 is indeed working to colorize the connectome ring in the manner I would consider correct.
Thanks for the intervention!
Paul
Hi Paul,
Sorry about that, could you please try the attached up-to-date version directly and let me know if you are still running into any issues? (this patch is for release 19c, to install it unzip this file and copy all of its contents to your conn distribution folder overwriting the files with the same name there)
Best
Alfonso