When you click on the gray areas, is the value 0 or just something very close to 0? You may need to set the lower threshold (default is 2). Also, I would recommend using freeview via tksurferfv (same command line as tksurfer)

On 11/4/2020 2:12 PM, Nelson, Eric wrote:

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Hello,

I am using FreeSurfer 7.1.1 to run LGI and have done so successfully. I am now trying to quality check my data using tksurfer as described on the wiki

/tksurfer my_subject_id lh inflated -overlay lh.pial_lgi/

However the LGI overlay is not covering the entirety of the inflated brain. Specifically the medial frontal surface and some subcortical are not measured for LGI.  Here is a link of the overlay images for a few subjects: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.dropbox.com/s/9pt8rti4yjudrza/LGI_QC.png?dl=0. I https://secure-web.cisco.com/1yytrZan4Ml7C4NJTkc91uplhrETEPm4MAwDFEYaEAXtVlSnzGTjs5BjzZZSDOtTgizZpSDnl3ThVIFkaiXv--DGYo5izF1yFMK4gbyOHaQIVo_20HarcOi_HT6zrv2m6X_pzP4BKEZbOmkD8UlglJjPZELhvw-kW4tNs_q2K97iR-nN8xvGyh2mHAgjXm9saalzD0cAqzMFUXXNDhGfoyA/https%3A%2F%2Fwww.dropbox.com%2Fs%2F9pt8rti4yjudrza%2FLGI_QC.png%3Fdl%3D0.%2520I%2520. I haven’t been able to find any images of what this overlay should look like so I don’t know if this is expected or if something has gone wrong with the processing. Any feedback would be greatly appreciated

Best,

Eric

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