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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
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