hanayik
commented
1 year ago Hi, this repo is not meant for FSL software support. It was a demo that never got past the work-in-progress stage. Please repost your question to the FSL mailing list here: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=fsl
From: zhaolei215 @.> Date: Wednesday, 22 November 2023 at 02:52 To: FMRIB-Software-Library/support @.> Cc: Subscribed @.***> Subject: [FMRIB-Software-Library/support] Extract the mean cortical thickness of brain regions (Issue #18)
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 don't know how to use fslstats correctly. I hope you can help me check if it's 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 sample_1_CorticalThinknessToMNI. nii. gz - ktemplate1uto-MNI. nii. gz - M>sample_1-MeanThinknessTemplate1. txt
Fslstats sample_1_CorticalThinknessToMNI. nii. gz - k template2uto-MNI. nii. gz - M>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.
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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 don't know how to use fslstats correctly. I hope you can help me check if it's 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