Cortical Thickness measures using different ways of processing

[arianafei]

Hi,

We are recently trying to get cortical thickness from freesurfer and converting them to 32k. A problem we notice is that after converting to 32k, all the cortical thickness values become negative. However, when we load freesurfer thickness files in freeview, everything appears normal. We wonder if merely inverting what we currently in 32k would be a good idea. Alternatively, we also calculated the Euclidean distance of pial and white after they have been converted into 32k space, which should be cortical thickness. However, when comparing the inverted values and the pial-white values, we find that there is some difference (shown by the scatter plot and correlation). In this case, has anyone ever had similar issues and have suggestions on which one to trust?

Thanks! correlation~0.94

[dngreve]

Please post this to the freesufer list

On 7/19/2022 5:44 PM, arianafei wrote:

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Hi,

We are recently trying to get cortical thickness from freesurfer and converting them to 32k. A problem we notice is that after converting to 32k, all the cortical thickness values become negative. However, when we load freesurfer thickness files in freeview, everything appears normal. We wonder if merely inverting what we currently in 32k would be a good idea. Alternatively, we also calculated the Euclidean distance of pial and white after they have been converted into 32k space, which should be cortical thickness. However, when comparing the inverted values and the pial-white values, we find that there is some difference (shown by the scatter plot and correlation). In this case, has anyone ever had similar issues and have suggestions on which one to trust?

Thanks! Screen Shot 2022-07-19 at 4 20 34 PM https://secure-web.cisco.com/1CmO3BFnwsdfWJUK2ToEk6iW0EHNYlZmPn3_lqYUHNRutC252mEHpSUYNhIBCmSsXO83yZAekLF9BN_ZrPOrWbTKjICrglcIHX9wO3U69WCnUF8xcaP77wHSYafDCcABvAK3cnUe_R6rdkjYiFxpC40SCkrPpc8ab8iBcsiPkON6Hut9y8udEoVGPv5rtnil0if4_5k91MqppDBnjT4QBFWAr7m3hSdqkzHSAToplbETpqgQbVWhPPLacFL0wL35baiGisAg6L1LICClkj74_KCJH0j1QmSFTsXM0d6rNm8PwsukkAADS7zukzW3uDV5e/https%3A%2F%2Fuser-images.githubusercontent.com%2F91152947%2F179853916-bf9b5ab1-4164-46da-85a7-a11a42dfb0d7.png correlation~0.94

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[buildqa]

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