Extract the mean cortical thickness of brain regions

[zhaolei215]

teacher
I obtained the corticalthickness.nii.gz file using antsCorticalThickness. sh and it has been converted to the MNI template space. Now, I want to extract the mean cortical thickness of brain regions. I found two types of brain maps, dk and dkt. The file name is IIT_ GM_ Desikan_ Atlas_ 256.nii.gz and IIT_ GM_ Destrieux_ Atlas_ 256.nii.gz.
I want to use these two brain maps to obtain the average cortical thickness, but I don't know how to use them correctly.
The following is the script code that I came up with. I hope you can help me check if it is correct:```
{#Convert dk to MNI space
AntsApplyTransforms - d 3
-i ${dk}
-r ${MNI_TEMPLATE}
-o "${OUT_DIR}/template1_to MNI. ni. gz"
-n Linear
-t ${DATA_DIR}/antsCorticalThickness/Template1ToMNIWarp.nii.gz
-t ${DATA_DIR}/antsCorticalThickness/Template1ToMNIAffine.txt
#Dkt conversion to MNI space
AntsApplyTransforms - d 3
-i ${dkt}
-r ${MNI_TEMPLATE}
-o "${OUT_DIR}/template2_to MNI. ni. gz"
-n Linear
-t ${DATA_DIR}/antsCorticalThickness/Template2ToMNIWarp.nii.gz
-t ${DATA_DIR}/antsCorticalThickness/Template2ToMNIAffine.txt
#Using FSL's fslstats command to calculate the average value of brain regions
Fslstats "${DATA_DIR}/sample_1_CorticalThinknessToMNI. nii. gz" - k "${OUTnDIR}/template1uto-MNI. nii. gz" - M>"${OUTnDIR}/sample_1-MeanThinknessTemplate1. txt"
Fslstats "${DATA_DIR}/sample_1_CorticalThinknessToMNI. nii. gz" - k "${OUTnDIR}/template2uto-MNI. nii. gz" - M>"${OUTnDIR}/sample_1-MeanThinknessTemplate2. txt"}

The websites for two brain atlases are: **https://www.nitrc.org/projects/iit/**

Sincerely thank you and hope to receive your reply.

[ntustison]

Yeah, you would just make sure each atlas is registered to your choice of space. YOu'd have to ask the FSL developers about the use of fslstats.

However, given all the questions that you have, you might be better served by our ANTsXNet version which doesn't require you to do all the registration steps. See here. Evaluation shows improved performance over the previous incarnation, i.e., antsCorticalThickness.sh.