No, there is a problem with your LUT (for the default, there might not be entries for all of your segs which is why you are not seeing them). I don't know what the problem is. Try making it a different way or doing it by hand in linux.
On 6/3/2022 1:20 PM, Benjamin Deck wrote:
External Email - Use Caution
Responding re: Douglas Greve
How exactly did you create the LUT? Eg, in windows using notepad? I'm thinking that there might be some hidden characters in there as the color is wrong. I did notice that your first entry had a value of 5 in the last column; usually this is 0 (not sure what it is for). What happens if you switch the LUT to the default? Do you get reasonable colors (even if the names are wrong)?
Reply:
I used a custom python script that creates a LUT for each subject. Then I ran dos2unix to ensure the line endings were appropriate.
If I load the default FS LUT only 2 ROIs are being labeled.
Does this mean that I have an issue with my mri_concat call?
Which is:
mri_concat --sum --f vols.txt --o sub_vols.mgz
Thanks, Ben
-- *Benjamin L. Deck* /Doctoral Student/ /Applied Cognitive and Brain Sciences/ /Department of Psychological and Brain Sciences/ /Drexel University/
https://secure-web.cisco.com/1orR-DWFSm7AzAYYcqvCSHmblQoGORO7YzkKJqo0iTu7-ysKMneqiJIB914MLo59YkJqozzyS-ZYvEmsjfYZ-WRPwN9DkX_AezdGhpvKU2LHZseaLjN_pqFfvqE9K_9Eb8jcrG_fy3Sqx_E1WWkgfvqxBpxdULKUdqoHpZSRz2HIjOFSI3kVrQ3I8AjZ2vJydm-kwNnameEcwcBoNrCTynvHwljQJ0JIK4xh1JYMxYqZ6SsJ21pyNj05itbv664ZDeltcN1_uI5hJ3ZiOWZkjRl--hlt4ymwEHoSXW4BnnavPb4pK9ZO-H1l6GKUnTNsDVGpDPvfgbErAM7j-puzDRQ/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dicon Virus-free. *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* www.avast.com https://secure-web.cisco.com/1Q_PewrE8ioL4nGaDXS3HygbqgAIyt7ilGvMJtVbT_Yof-G81xhAIQ5t31xNREI6mrNHRJCGChvOl_UNEEkz3Mn8y2jlcNAW3b_5DTtubD6H8MJrvMDQR0Rt0Qub68uwKV6Tzf1qZ3jQ0dSlRAoI6RezN59eD__Xhlk30lC-rrHfjqNjH4T66U3h8S-Jb4wjx_HjNFN9b2fFOuYGMQB6CabooHcjX5tNh_Gigk_s0bD3zgpeZ-PA2vU0EempK4Fc9Smb_WMFPL_KEKM-rdXOxA6cTVPTZhNXGWoaBS0e5MH8vfJonY5jWTDzOry2YBYKCWjty0zlrxDbSRT29vo5YEA/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dlink
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer