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:

External Email - Use Caution

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. 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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