Please try using the 1mm version of the segmentation in FreeSurfer space. Cheers, /Eugenio
-- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Jessica Bourgin <jessica.bour...@univ-smb.fr> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Thursday, 8 August 2019 at 11:58 To: freesurfer <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space External Email - Use Caution 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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