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Hi,
I was using version 6.0.0 but I have just tried 7.1.1 and it works fine. Thank you!
Amanda ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wang, Ruopeng RWANG4@mgh.harvard.edu Sent: 23 September 2021 16:56 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Customising overlay
You don't often get email from rwang4@mgh.harvard.edu. Learn why this is importanthttp://secure-web.cisco.com/1s9Gk6oIUjBZIyl-B7jw8KdllSqDTnZKvoMebAeIJpJHh0DbJJy9BVCZWPbO6za6RArW63BQ5I96zvGvWmRqzrEQgEFwOzP5lx1T7TR8QjWxtrG_h5NX2CIx-XM1PXC33oPcEb9bik8J--B3msp_PsKLMZbLJsRm_2zkYNkHmfZKcZwJMU2fsHGeQVEkvXwuzHUMdZ6O2tdnSDxS4GBjwYx24uPjSC_xbaCqbv3zo43xZoRAu4KD5WAPRj-bGil13h2Kvv6A5fkEbEeDfDLEcWw/http%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification What version of freesurfer are you using? I tried the latest freeview build and had no problem inserting colors at arbitrary value for customized color option.
Best, Ruopeng
On Sep 23, 2021, at 9:00 AM, Worker, Amanda <amanda.worker@kcl.ac.ukmailto:amanda.worker@kcl.ac.uk> wrote:
External Email - Use Caution
External Email - Use Caution
Dear FreeSurfer Developers,
I am attempting to create some figures which display regional (Destrieux atlas) values which are typically in the range of 0-10. I would like to have an inflated brain with those regional values overlaid, for both patients and healthy controls. In total there will be four independent figures. The problem I am having is that the range of values is different for each overlay e.g. overlay 1 regional value range from 0-3, overlay 2 regional values range from 0-8, which means that the colour scales are on different scales. I would like to find a way to manually set the scale to 0-10 for each overlay, regardless of the actual values that exist within the overlay file.
I am currently using the below command to load the overlay and then manually configuring the colour scale via the custom option, but I cannot add a point that is outside the range of values that exist in that overlay. I hope this makes sense and I would appreciate any advice you can give on how to achieve consistent colour scales for different overlays.
freeview -f /software/system/freesurfer/freesurfer-6.0.0/subjects/fsaverage/surf/rh.inflated:overlay=rh_pcnt_neg_control_01.mgz:overlay_method=linearopaque:overlay_threshold=0,5,10
Kind regards,
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