External Email - Use Caution
?
Dear Freesurfer Team,
we would like to perform a volumetric analysis in Parkinson's disease using freesurfer, and we have previously used recon all to perform tha surface based analysis and automate segmentation.
We would also like to extract the different volumes of striatal parcellation using the Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz.
However, we can't find how to perform this parcellation, and how to add it to the recon all steps?
Thank you very much for your help!
?
Ana Marques MD, PhD Service de Neurologie Hopital Gabriel-Montpied CHRU Clermont-Ferrand ar_marques@chu-clermontferrand.frmailto:ar_marques@chu-clermontferrand.fr TEL: 04 73 751 600 FAX: 04 73 751 596
External Email - Use Caution
Hi Ana,
To transform the Choi's striatal atlas to your individual subject, Here's a (non-ideal) suggestion I previously suggested to another user:
1) Assuming you are quite happy with the freesurfer striatal parcellation in your individual subjects, then I am assuming freesurfer nonlinear registration (talairach.m3z) is working quite well. Talairach.m3z warps your subject to an internal freesurfer space (kinda like MNI305, but not quite). Let's say the freesurfer recon-all output is at <something>/SUBJECT_FS/
2) Run the MNI152 1mm template (the one from FSL) through recon-all. Recon-all will give you a Talairach.m3z that allows you to map the MNI152 1mm template to the internal freesurfer space. Let's say the freesurfer recon-all output is at <something>/MNI152_FS/
3) Then do the following:
a) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:
setenv SUBJECTS_DIR <something> mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS --targ
$FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Choi_atlas_freesurfer_internal_space.nii.gz --interp nearest
b) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your subject:
setenv SUBJECTS_DIR <something> mri_vol2vol --mov $SUBJECTS_DIR/AD_SUBJECT_FS/mri/norm.mgz --s
AD_SUBJECT_FS --targ Choi_atlas_freesurfer_internal_space.nii.gz --m3z talairach.m3z --o Choi_atlas_AD_subject.nii.gz --interp nearest --inv-morph
This is not optimal because of the double interpolation. You might want to use the MNI template instead of the Choi_atlas to test the above, so you can check the goodness of the warp. The final warped MNI template should hopefully look identical to your subject. If that works, then use the Choi_atlas. Note that mri_vol2vol does not work properly for talairach.m3z below version 5, so you should use version 5x mri_vol2vol. Regards, Thomas
On Tue, Feb 16, 2021 at 12:02 AM Marques Ana-raquel < ar_marques@chu-clermontferrand.fr> wrote:
External Email - Use CautionDear Freesurfer Team,
we would like to perform a volumetric analysis in Parkinson's disease using freesurfer, and we have previously used recon all to perform tha surface based analysis and automate segmentation.
We would also like to extract the different volumes of striatal parcellation using the Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz.
However, we can't find how to perform this parcellation, and how to add it to the recon all steps?
Thank you very much for your help!
Ana Marques MD, PhD Service de Neurologie Hopital Gabriel-Montpied CHRU Clermont-Ferrand ar_marques@chu-clermontferrand.fr TEL: 04 73 751 600 FAX: 04 73 751 596 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ky2M__2Q83PHmm85e8X04i_6D3Ih7BP_TXAiDg22QWgeej...
External Email - Use Caution
Thank you very much for your help Thomas!!
Ana Marques Praticien Hospitalier Service de Neurologie Hopital Gabriel-Montpied CHRU Clermont-Ferrand ar_marques@chu-clermontferrand.frmailto:ar_marques@chu-clermontferrand.fr TEL: 04 73 751 600 FAX: 04 73 751 596 ________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Thomas Yeo ythomas@csail.mit.edu Envoyé : mardi 16 février 2021 01:02 À : Freesurfer support list Objet : Re: [Freesurfer] striatal parcellation
External Email - Use Caution
Hi Ana,
To transform the Choi's striatal atlas to your individual subject, Here's a (non-ideal) suggestion I previously suggested to another user:
1) Assuming you are quite happy with the freesurfer striatal parcellation in your individual subjects, then I am assuming freesurfer nonlinear registration (talairach.m3z) is working quite well. Talairach.m3z warps your subject to an internal freesurfer space (kinda like MNI305, but not quite). Let's say the freesurfer recon-all output is at <something>/SUBJECT_FS/
2) Run the MNI152 1mm template (the one from FSL) through recon-all. Recon-all will give you a Talairach.m3z that allows you to map the MNI152 1mm template to the internal freesurfer space. Let's say the freesurfer recon-all output is at <something>/MNI152_FS/
3) Then do the following:
a) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:
setenv SUBJECTS_DIR <something> mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Choi_atlas_freesurfer_internal_space.nii.gz --interp nearest
b) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your subject:
setenv SUBJECTS_DIR <something> mri_vol2vol --mov $SUBJECTS_DIR/AD_SUBJECT_FS/mri/norm.mgz --s AD_SUBJECT_FS --targ Choi_atlas_freesurfer_internal_space.nii.gz --m3z talairach.m3z --o Choi_atlas_AD_subject.nii.gz --interp nearest --inv-morph
This is not optimal because of the double interpolation. You might want to use the MNI template instead of the Choi_atlas to test the above, so you can check the goodness of the warp. The final warped MNI template should hopefully look identical to your subject. If that works, then use the Choi_atlas. Note that mri_vol2vol does not work properly for talairach.m3z below version 5, so you should use version 5x mri_vol2vol.
Regards, Thomas
On Tue, Feb 16, 2021 at 12:02 AM Marques Ana-raquel <ar_marques@chu-clermontferrand.frmailto:ar_marques@chu-clermontferrand.fr> wrote:
External Email - Use Caution
Dear Freesurfer Team,
we would like to perform a volumetric analysis in Parkinson's disease using freesurfer, and we have previously used recon all to perform tha surface based analysis and automate segmentation.
We would also like to extract the different volumes of striatal parcellation using the Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz.
However, we can't find how to perform this parcellation, and how to add it to the recon all steps?
Thank you very much for your help!
Ana Marques MD, PhD Service de Neurologie Hopital Gabriel-Montpied CHRU Clermont-Ferrand ar_marques@chu-clermontferrand.frmailto:ar_marques@chu-clermontferrand.fr TEL: 04 73 751 600 FAX: 04 73 751 596 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1bvKz03BrZcZsNzn2KFFAnZX-e0Rfg0dbJglxZp21F6pJ8Q...https://secure-web.cisco.com/1ky2M__2Q83PHmm85e8X04i_6D3Ih7BP_TXAiDg22QWgeejkZl0o1gg97FhDak96qlKpDdy9REGY41KUyxt2FdLTW4-j6xONpCHt8VTXZNG6Kn1i0nXgeiJpH0Xl7HvB0mZVtw0NPBj1kL6ZdHNgYM2YYiHSXTiEbPIbn7nqcZOPK6cergv6Xo6cq5ra51o9fDACFYVxTOXkKAOOfFGQj6dH4SllbxdmomcIphtKa4-Y5zf_Fj00RpDAobAqJCIfqQhwY1vMX1Q5gwSoGSlLzzA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
External Email - Use Caution
Dear Freesurfer Team,
We would like to perform a striatal parcellation in PD patients and controls using the Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz.
We followed the instructions below which allowed us to transform the Choi's striatal atlas to our individual subjects, Here's a (non-ideal) suggestion I previously suggested to another user:
1) Assuming you are quite happy with the freesurfer striatal parcellation in your individual subjects, then I am assuming freesurfer nonlinear registration (talairach.m3z) is working quite well. Talairach.m3z warps your subject to an internal freesurfer space (kinda like MNI305, but not quite). Let's say the freesurfer recon-all output is at <something>/SUBJECT_FS/
2) Run the MNI152 1mm template (the one from FSL) through recon-all. Recon-all will give you a Talairach.m3z that allows you to map the MNI152 1mm template to the internal freesurfer space. Let's say the freesurfer recon-all output is at <something>/MNI152_FS/
3) Then do the following:
a) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:
setenv SUBJECTS_DIR <something> mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Choi_atlas_freesurfer_internal_space.nii.gz --interp nearest
b) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your subject:
setenv SUBJECTS_DIR <something> mri_vol2vol --mov $SUBJECTS_DIR/AD_SUBJECT_FS/mri/norm.mgz --s AD_SUBJECT_FS --targ Choi_atlas_freesurfer_internal_space.nii.gz --m3z talairach.m3z --o Choi_atlas_AD_subject.nii.gz --interp nearest --inv-morph
This worked very well (but we have to perform this indicidually for all our subjects). OUr next question is : how can we obtain an "aseg.stat" file from this striatal parcellation, in order to have the volumes of the 7 different régions for each subject?
Thanks a lot for yor help!!
Ana
Ana Marques MD, PhD Praticien Hospitalier Service de Neurologie Hopital Gabriel-Montpied CHRU Clermont-Ferrand ar_marques@chu-clermontferrand.frmailto:ar_marques@chu-clermontferrand.fr TEL: 04 73 751 600 FAX: 04 73 751 596 ________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Thomas Yeo ythomas@csail.mit.edu Envoyé : mardi 16 février 2021 01:02 À : Freesurfer support list Objet : Re: [Freesurfer] striatal parcellation
External Email - Use Caution
Hi Ana,
To transform the Choi's striatal atlas to your individual subject, Here's a (non-ideal) suggestion I previously suggested to another user:
1) Assuming you are quite happy with the freesurfer striatal parcellation in your individual subjects, then I am assuming freesurfer nonlinear registration (talairach.m3z) is working quite well. Talairach.m3z warps your subject to an internal freesurfer space (kinda like MNI305, but not quite). Let's say the freesurfer recon-all output is at <something>/SUBJECT_FS/
2) Run the MNI152 1mm template (the one from FSL) through recon-all. Recon-all will give you a Talairach.m3z that allows you to map the MNI152 1mm template to the internal freesurfer space. Let's say the freesurfer recon-all output is at <something>/MNI152_FS/
3) Then do the following:
a) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:
setenv SUBJECTS_DIR <something> mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Choi_atlas_freesurfer_internal_space.nii.gz --interp nearest
b) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your subject:
setenv SUBJECTS_DIR <something> mri_vol2vol --mov $SUBJECTS_DIR/AD_SUBJECT_FS/mri/norm.mgz --s AD_SUBJECT_FS --targ Choi_atlas_freesurfer_internal_space.nii.gz --m3z talairach.m3z --o Choi_atlas_AD_subject.nii.gz --interp nearest --inv-morph
This is not optimal because of the double interpolation. You might want to use the MNI template instead of the Choi_atlas to test the above, so you can check the goodness of the warp. The final warped MNI template should hopefully look identical to your subject. If that works, then use the Choi_atlas. Note that mri_vol2vol does not work properly for talairach.m3z below version 5, so you should use version 5x mri_vol2vol.
Regards, Thomas
On Tue, Feb 16, 2021 at 12:02 AM Marques Ana-raquel <ar_marques@chu-clermontferrand.frmailto:ar_marques@chu-clermontferrand.fr> wrote:
External Email - Use Caution
Dear Freesurfer Team,
we would like to perform a volumetric analysis in Parkinson's disease using freesurfer, and we have previously used recon all to perform tha surface based analysis and automate segmentation.
We would also like to extract the different volumes of striatal parcellation using the Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz.
However, we can't find how to perform this parcellation, and how to add it to the recon all steps?
Thank you very much for your help!
Ana Marques MD, PhD Service de Neurologie Hopital Gabriel-Montpied CHRU Clermont-Ferrand ar_marques@chu-clermontferrand.frmailto:ar_marques@chu-clermontferrand.fr TEL: 04 73 751 600 FAX: 04 73 751 596 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1_UFLDzPXd_JrEwuhvlUIqpOhrHsgTsmG9-R1lBw45BCbPU...https://secure-web.cisco.com/1ky2M__2Q83PHmm85e8X04i_6D3Ih7BP_TXAiDg22QWgeejkZl0o1gg97FhDak96qlKpDdy9REGY41KUyxt2FdLTW4-j6xONpCHt8VTXZNG6Kn1i0nXgeiJpH0Xl7HvB0mZVtw0NPBj1kL6ZdHNgYM2YYiHSXTiEbPIbn7nqcZOPK6cergv6Xo6cq5ra51o9fDACFYVxTOXkKAOOfFGQj6dH4SllbxdmomcIphtKa4-Y5zf_Fj00RpDAobAqJCIfqQhwY1vMX1Q5gwSoGSlLzzA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
For the aseg.stats, you can run mri_segstats. Look in recon-all.cmd for the command that creates the aseg.stats file and change the input and output
On 4/7/2021 8:24 AM, Marques Ana-raquel wrote:
External Email - Use Caution
Dear Freesurfer Team,
We would like to perform a striatal parcellation in PD patients and controls using the Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz.
We followed the instructions below which allowed us to transform the Choi's striatal atlas to our individual subjects, Here's a (non-ideal) suggestion I previously suggested to another user:
- Assuming you are quite happy with the freesurfer striatal
parcellation in your individual subjects, then I am assuming freesurfer nonlinear registration (talairach.m3z) is working quite well. Talairach.m3z warps your subject to an internal freesurfer space (kinda like MNI305, but not quite). Let's say the freesurfer recon-all output is at <something>/SUBJECT_FS/
- Run the MNI152 1mm template (the one from FSL) through recon-all.
Recon-all will give you a Talairach.m3z that allows you to map the MNI152 1mm template to the internal freesurfer space. Let's say the freesurfer recon-all output is at <something>/MNI152_FS/
- Then do the following:
a) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:
setenv SUBJECTS_DIR <something> mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS --targ
$FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Choi_atlas_freesurfer_internal_space.nii.gz --interp nearest
b) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your subject:
setenv SUBJECTS_DIR <something> mri_vol2vol --mov $SUBJECTS_DIR/AD_SUBJECT_FS/mri/norm.mgz --s
AD_SUBJECT_FS --targ Choi_atlas_freesurfer_internal_space.nii.gz --m3z talairach.m3z --o Choi_atlas_AD_subject.nii.gz --interp nearest --inv-morph This worked very well (but we have to perform this indicidually for all our subjects). OUr next question is : *how can we obtain an "aseg.stat" file from this striatal parcellation, in order to have the volumes of the 7 different régions for each subject?* Thanks a lot for yor help!! Ana Ana Marques MD, PhD Praticien Hospitalier Service de Neurologie Hopital Gabriel-Montpied CHRU Clermont-Ferrand ar_marques@chu-clermontferrand.fr mailto:ar_marques@chu-clermontferrand.fr TEL: 04 73 751 600 FAX: 04 73 751 596
*De :* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Thomas Yeo ythomas@csail.mit.edu *Envoyé :* mardi 16 février 2021 01:02 *À :* Freesurfer support list *Objet :* Re: [Freesurfer] striatal parcellation
External Email - Use Caution
Hi Ana,
To transform the Choi's striatal atlas to your individual subject, Here's a (non-ideal) suggestion I previously suggested to another user:
- Assuming you are quite happy with the freesurfer striatal
parcellation in your individual subjects, then I am assuming freesurfer nonlinear registration (talairach.m3z) is working quite well. Talairach.m3z warps your subject to an internal freesurfer space (kinda like MNI305, but not quite). Let's say the freesurfer recon-all output is at <something>/SUBJECT_FS/
- Run the MNI152 1mm template (the one from FSL) through recon-all.
Recon-all will give you a Talairach.m3z that allows you to map the MNI152 1mm template to the internal freesurfer space. Let's say the freesurfer recon-all output is at <something>/MNI152_FS/
- Then do the following:
a) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:
setenv SUBJECTS_DIR <something> mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS --targ
$FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Choi_atlas_freesurfer_internal_space.nii.gz --interp nearest
b) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your subject:
setenv SUBJECTS_DIR <something> mri_vol2vol --mov $SUBJECTS_DIR/AD_SUBJECT_FS/mri/norm.mgz --s
AD_SUBJECT_FS --targ Choi_atlas_freesurfer_internal_space.nii.gz --m3z talairach.m3z --o Choi_atlas_AD_subject.nii.gz --interp nearest --inv-morph
This is not optimal because of the double interpolation. You might want to use the MNI template instead of the Choi_atlas to test the above, so you can check the goodness of the warp. The final warped MNI template should hopefully look identical to your subject. If that works, then use the Choi_atlas. Note that mri_vol2vol does not work properly for talairach.m3z below version 5, so you should use version 5x mri_vol2vol.
Regards, Thomas
On Tue, Feb 16, 2021 at 12:02 AM Marques Ana-raquel <ar_marques@chu-clermontferrand.fr mailto:ar_marques@chu-clermontferrand.fr> wrote:
External Email - Use Caution Dear Freesurfer Team, we would like to perform a volumetric analysis in Parkinson's disease using freesurfer, and we have previously used recon all to perform tha surface based analysis and automate segmentation. We would also like to extract the different volumes of striatal parcellation using the Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz. However, we can't find how to perform this parcellation, and how to add it to the recon all steps? Thank you very much for your help! Ana Marques MD, PhD Service de Neurologie Hopital Gabriel-Montpied CHRU Clermont-Ferrand ar_marques@chu-clermontferrand.fr <mailto:ar_marques@chu-clermontferrand.fr> TEL: 04 73 751 600 FAX: 04 73 751 596 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1ky2M__2Q83PHmm85e8X04i_6D3Ih7BP_TXAiDg22QWgeejkZl0o1gg97FhDak96qlKpDdy9REGY41KUyxt2FdLTW4-j6xONpCHt8VTXZNG6Kn1i0nXgeiJpH0Xl7HvB0mZVtw0NPBj1kL6ZdHNgYM2YYiHSXTiEbPIbn7nqcZOPK6cergv6Xo6cq5ra51o9fDACFYVxTOXkKAOOfFGQj6dH4SllbxdmomcIphtKa4-Y5zf_Fj00RpDAobAqJCIfqQhwY1vMX1Q5gwSoGSlLzzA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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