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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,
Amanda
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,
Amanda _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1Mvs087uVuGMwQ43VKbZ4KQUC8sXdfwJ_HJN63344pj1RZd...
External Email - Use Caution
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,
Amanda _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1Mvs087uVuGMwQ43VKbZ4KQUC8sXdfwJ_HJN63344pj1RZd...https://secure-web.cisco.com/1nDkoAYU1WruFiFbF_xvio3zzurFit9BM4T2Yzgm7K2PhqpKKaUlxx7Zy-xnMPhSReix36V8H-D71vNkkBjWu-6jPGTR0sc2pKrctM-RtIISobtl94VVaBZX1ofAyT2SMekf9ICklz2fjlIEPzVMndE9NDk3J2l8TOApSGW8Iy7ZVQZ9WGJ6f6ZRfotgWxQUWNQR1OfvO-XbHd4taI1gBTYCFsDZzPd6e5GqrE2b97K-t3mu_rE4rQ4CFTmlVo_O2E0Rq5kQ6NE-WviJJ9etPcw/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1Mvs087uVuGMwQ43VKbZ4KQUC8sXdfwJ_HJN63344pj1RZdNgj3LOa62UZoVaTOMEheuzBeobIvsoNbJzkpmwsNXB3DmaDQRXq-UoMpQne6KYNlErDKFALpp4l65DOiL-RIqtoF016NEtQcI4xMfhkoCwiqN1yQyLfj7FDvAr25wnulgZji0vaisuA3BQRRUOb9RrgT34Od8lnN8pQIrZ2hI4AVwNLOt5C9dW5wpcYDB6AzstorI-BKRO5XtKjdjYGhTtp1erj5NqQefOeqHKNA%252Fhttps%25253A%25252F%25252Fmail.nmr.mgh.harvard.edu%25252Fmailman%25252Flistinfo%25252Ffreesurfer%26data%3D04%257C01%257Camanda.worker%2540kcl.ac.uk%257C63041bed3a8e46bb874908d97eaadfaa%257C8370cf1416f34c16b83c724071654356%257C0%257C0%257C637680094657111886%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3D5IJHJuK8JLgs%252BaZhZ1ISMdww2kboWizZnR1Mbjkx%252F5s%253D%26reserved%3D0
freesurfer@nmr.mgh.harvard.edu
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Wang, Ruopeng -
Worker, Amanda