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Dear Juan Eugenio,

Thank you for these precisions.

Following the guidelines of FSL, I computed the following sequence on my structural image :

bet my_structural my_betted_structural flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in my_betted_structural -omat my_affine_transf.mat fnirt --in=my_structural --aff=my_affine_transf.mat --cout=my_nonlinear_transf --config=T1_2_MNI152_2mm applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=my_structural --warp=my_nonlinear_transf --out=my_warped_structural

The warped structural image overlapped nicely with the atlas.

However, when I compute the following command on the segmentations :

applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=freesurfer/lh.hippoAmygLabels-T1.v21.nii.gz --warp=my_nonlinear_transf --out=my_warped_lh applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=freesurfer/rh.hippoAmygLabels-T1.v21.nii.gz --warp=my_nonlinear_transf --out=my_warped_rh

The segmentations do not appear on the atlas nor the structural image.

Do you know how to solve this problem ?

Thanks for your help.

PS: I used FSL for registration because I don't know how to do that with Freesurfer.

Jessica BOURGIN Laboratoire de Psychologie et Neurocognition CNRS UMR 5105 Université Savoie Mont Blanc (USMB) BP 1104 73011 Chambery Cedex France