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Hello Freesurfer developers,
For the purpose of reporting ROIs in my article, I need a list of X Y Z coordinates in MNI space for all the labels in the Destrieux atlas. I came across a previous post with the following steps:
Step 1: mri_annotation2label --subject fsaverage --hemi lh --annotation aparc.a2009s --outdir ~/myproject/processed/tmp
Step 2: mri_surfcluster --in ~/myproject/processed/fsaverage/surf/lh.thickness --clabel lh.G_pariet_inf-Supramar.label --sum ~/myproject/processed/tmp/sum.lh_G_pariet_inf-supramar --centroid --thmin 0 --hemi lh --subject fsaverage --nofixmni
Q1: All the ROIs appeared to have identical MNI coordinates. what should I do?
Q2: For reporting the list of X Y Z coordinates in MNI space for all the labels in aseg.stats ROIs, What should I change?
Thank you in advance, Best regards, Hengameh
External Email - Use Caution
Hello Freesurfer developers,
I have deadline time to report these coordinates.
I greatly appreciate your help and I'm looking forward to your kind response.
Best regards, Hengameh
On Fri, Nov 20, 2020 at 11:20 AM Hengameh Marzbani marzbani91@gmail.com wrote:
Hello Freesurfer developers,
For the purpose of reporting ROIs in my article, I need a list of X Y Z coordinates in MNI space for all the labels in the Destrieux atlas. I came across a previous post with the following steps:
Step 1: mri_annotation2label --subject fsaverage --hemi lh --annotation aparc.a2009s --outdir ~/myproject/processed/tmp
Step 2: mri_surfcluster --in ~/myproject/processed/fsaverage/surf/lh.thickness --clabel lh.G_pariet_inf-Supramar.label --sum ~/myproject/processed/tmp/sum.lh_G_pariet_inf-supramar --centroid --thmin 0 --hemi lh --subject fsaverage --nofixmni
Q1: All the ROIs appeared to have identical MNI coordinates. what should I do?
Q2: For reporting the list of X Y Z coordinates in MNI space for all the labels in aseg.stats ROIs, What should I change?
Thank you in advance, Best regards, Hengameh
It is probably easier to just run recon-all on the mni152, then use mri_segcentroids on aparc.a2009s to extract the centroids
On 11/20/2020 2:50 AM, Hengameh Marzbani wrote:
External Email - Use Caution
Hello Freesurfer developers,
For the purpose of reporting ROIs in my article, I need a list of X Y Z coordinates in MNI space for all the labels in the Destrieux atlas. I came across a previous post with the following steps:
Step 1: mri_annotation2label --subject fsaverage --hemi lh --annotation aparc.a2009s --outdir ~/myproject/processed/tmp
Step 2: mri_surfcluster --in ~/myproject/processed/fsaverage/surf/lh.thickness --clabel lh.G_pariet_inf-Supramar.label --sum ~/myproject/processed/tmp/sum.lh_G_pariet_inf-supramar --centroid --thmin 0 --hemi lh --subject fsaverage --nofixmni
Q1: All the ROIs appeared to have identical MNI coordinates. what should I do?
Q2: For reporting the list of X Y Z coordinates in MNI space for all the labels in aseg.stats ROIs, What should I change?
Thank you in advance, Best regards, Hengameh
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Greve, Douglas N.,Ph.D. -
Hengameh Marzbani