Date: 2021-06-01 22:35 |
Priority: more information 3 |
Submitted By:
Yogatheesan Varatharajah (varatha2)
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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)
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Response
Message |
Date: 2021-06-02 15:01
Sender: Yogatheesan Varatharajah
Hi Chris,
Attached is the overlay image I am using.
Thanks.
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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
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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).
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Attached Files:
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Changes:
Field |
Old Value |
Date |
By |
File Added | 1146: mni152_2009.mz3 | 2021-06-02 15:01 | varatha2 |
New Message | | 2021-06-02 15:01 | varatha2 |
File Added | 1145: sub1_alpha1_eLORETA.nii.gz | 2021-06-02 13:44 | varatha2 |
New Message | | 2021-06-02 13:44 | varatha2 |
File Added | 1144: invert.png | 2021-06-02 12:51 | crlab |
New Message | | 2021-06-02 12:51 | crlab |
File Added | 1143: Screen Shot 2021-06-01 at 5.33.41 PM.png | 2021-06-01 22:35 | varatha2 |
File Added | 1142: Screen Shot 2021-06-01 at 5.32.53 PM.png | 2021-06-01 22:35 | varatha2 | |
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