[#9915] Colormap getting reversed in surfice

Please log in

State: more information
Open
Date:
2021-06-01 22:35
Priority: more information
3
Submitted By:
Yogatheesan Varatharajah (varatha2)
Assigned To: more information
Nobody (None)
Hardware: 
Macintosh
Product: 
None
Operating System: 
MacOS X
Component: 
None
Version: 
v1.1
Severity: 
major
Summary: more information
Colormap getting reversed in surfice

Detailed description

Hi,
I am working on EEG source imaging. I generated nifti images using the MNE python library and tried to view them using multiple viewers.
The image looks fine in MRICron. However, the surfice view is completely different than expected. Any idea why this might happen?
I am overlaying on the MNI152 mesh.

Thanks

(Both images are attached)

Response

Message

Date: 2021-06-02 15:01
Sender: Yogatheesan Varatharajah

Hi Chris,
Attached is the overlay image I am using.

Thanks.


Date: 2021-06-02 13:44
Sender: Yogatheesan Varatharajah

Hi Chris,
Thanks for your response. 
But I am not sure if color scale inversion is the solution.
For context, the source image was generated from eyes closed EEG segments. My expectation is that we should see higher values in the occipital regions which we do see in the MRI Cron version. For some reason, we do not see that in surfice. Instead, we see higher values in the basal area. I'm wondering if there is a rotation issue (something to do with the niffi header). I am attaching the original nifti image if it can be of help.
The image I am viewing is in MNI space and the source space is on freesurfer average template. Any help would be appreciated.

Thanks
Yoga


Date: 2021-06-02 12:51
Sender: Chris Rorden

You have several options to control colors, all controlled in the "Overlays" panel.
 1. Choose the brightest and darkest color range. (e.g. 2..12)
 2. Choose the color scheme from the drop down menu (e.g. "Red-Yellow")
 3. You can press "Options" and "Invert colors" if you want the color range reversed, which is often useful when your color range is negative (e.g. making more extreme values more salient).

Attached Files:

Name Download
Screen Shot 2021-06-01 at 5.32.53 PM.png Download
Screen Shot 2021-06-01 at 5.33.41 PM.png Download
invert.png Download
sub1_alpha1_eLORETA.nii.gz Download
mni152_2009.mz3 Download

Changes:

Field Old Value Date By
File Added1146: mni152_2009.mz32021-06-02 15:01varatha2
New Message2021-06-02 15:01varatha2
File Added1145: sub1_alpha1_eLORETA.nii.gz2021-06-02 13:44varatha2
New Message2021-06-02 13:44varatha2
File Added1144: invert.png2021-06-02 12:51crlab
New Message2021-06-02 12:51crlab
File Added1143: Screen Shot 2021-06-01 at 5.33.41 PM.png2021-06-01 22:35varatha2
File Added1142: Screen Shot 2021-06-01 at 5.32.53 PM.png2021-06-01 22:35varatha2