Hello, I have yet another, likely obvious, question and I apologize if this is answered elsewhere. I ran the below series of functions to apply the HCP-MM1 (Glasser) atlas to the FreeSurfer output. I was able to produce an annotation file that had the labels in the right locations and mapping.
Yet, when I look at the output HCP-MMP1.mgz and HCP-MMP1+aseg.mgz files in FreeView or 3DSlicer, the old DKT FreeSurfer labels are applied to the brain labels (which are inaccurate). Is there an additional step I need to convert the labels such as using a modified HCP-MMP1 LUT look up table (such as linked herehttps://github.com/MRtrix3/mrtrix3/issues/1279)?
using the HCP-MMP1 annotation files: https://figshare.com/articles/dataset/HCP-MMP1_0_projected_on_fsaverage/3498...
And the use of mri_surf2volseg in the following sequence: https://github.com/ftadel/IntrAnat/issues/7#issuecomment-768996270
Thank you for any and all help, Angelique
Can you send the command line you used and the terminal output?
On 10/25/2022 8:19 PM, Paulk, Angelique C.,PhD wrote:
Hello, I have yet another, likely obvious, question and I apologize if this is answered elsewhere. I ran the below series of functions to apply the HCP-MM1 (Glasser) atlas to the FreeSurfer output. I was able to produce an annotation file that had the labels in the right locations and mapping.
Yet, when I look at the output HCP-MMP1.mgz and HCP-MMP1+aseg.mgz files in FreeView or 3DSlicer, the old DKT FreeSurfer labels are applied to the brain labels (which are inaccurate). Is there an additional step I need to convert the labels such as using a modified HCP-MMP1 LUT look up table (such as linked here https://github.com/MRtrix3/mrtrix3/issues/1279)?
using the HCP-MMP1 annotation files: https://figshare.com/articles/dataset/HCP-MMP1_0_projected_on_fsaverage/3498...
And the use of mri_surf2volseg in the following sequence: https://github.com/ftadel/IntrAnat/issues/7#issuecomment-768996270
Thank you for any and all help, Angelique
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Paulk, Angelique C.,PhD