ntustison
commented
9 months ago 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.
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 ${DATADIR}/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 ${DATADIR}/antsCorticalThickness/Template2ToMNIAffine.txt #Using FSL's fslstats command to calculate the average value of brain regions _Fslstats "${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}/sample1-MeanThinknessTemplate2. txt"}