Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space
External Email - Use Caution It seems to work. Thanks a lot ! Jessica BOURGIN Laboratoire de Psychologie et Neurocognition CNRS UMR 5105 Université Savoie Mont Blanc (USMB) BP 1104 73011 Chambery Cedex France ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space
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: on behalf of Jessica Bourgin
Reply-To: Freesurfer support list
Date: Thursday, 8 August 2019 at 11:58
To: freesurfer
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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space
Dear Jessica, You can register your image to the atlas, and then apply the same transform to the segmentations (“propagate”). That will bring the segmentations to atlas (Brainnetome) space. I hope this helps, /E -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Jessica Bourgin Reply-To: Freesurfer support list Date: Wednesday, 7 August 2019 at 13:44 To: freesurfer Subject: Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space External Email - Use Caution Dear Juan Eugenio, Thanks a lot for your quick response. I don't understand what you mean exactly by "propagate the hard segmentations". And when you say to register the subjects to the Brainnetome, do you mean replace the atlas used by recon-all to do that ? (sorry, I am currently a PhD student with little experience in neuroimaging). You also mention that the transformation is not trivial. But do you think this is "correct" to make it ? Thanks for your help ! Cheers, Jessica BOURGIN Laboratoire de Psychologie et Neurocognition CNRS UMR 5105 Université Savoie Mont Blanc (USMB) BP 1104 73011 Chambery Cedex France ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space
External Email - Use Caution Dear Juan Eugenio, Thanks a lot for your quick response. I don't understand what you mean exactly by "propagate the hard segmentations". And when you say to register the subjects to the Brainnetome, do you mean replace the atlas used by recon-all to do that ? (sorry, I am currently a PhD student with little experience in neuroimaging). You also mention that the transformation is not trivial. But do you think this is "correct" to make it ? Thanks for your help ! Cheers, Jessica BOURGIN Laboratoire de Psychologie et Neurocognition CNRS UMR 5105 Université Savoie Mont Blanc (USMB) BP 1104 73011 Chambery Cedex France ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space
Dear Jessica, There is no intensity image associated with the atlases, so this is not trivial. I guess you could register your subjects to the atlas, and propagate the hard segmentations? Cheers, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Jessica Bourgin Reply-To: Freesurfer support list Date: Wednesday, 7 August 2019 at 04:49 To: freesurfer Subject: [Freesurfer] Transform hippocampal/amygdala segmentation to another space External Email - Use Caution Dear all, I would like to use the Hippocampal Subfields and Nuclei Of Amygdala tool concomitantly with the Brainnetome Atlas for a resting-state analysis. For this purpose, I need the hippocampal/amygdala nuclei to be in the same space as the Brainnetome. Can you advise me on the method to use to transform the segmentation to another space ? Thank you in advance for your help. Best regards, Jessica BOURGIN Laboratoire de Psychologie et Neurocognition CNRS UMR 5105 Université Savoie Mont Blanc (USMB) BP 1104 73011 Chambery Cedex France ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
