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-bounces@nmr.mgh.harvard.edu> on behalf of Jessica Bourgin <jessica.bourgin@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