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Hello fellow Freesurfer users,
I am attempting to reproduce the analysis conducted by Parker et al. in their 2018 paper, “Cortical microstructure in young onset Alzheimer's disease using neurite orientation dispersion and density imaging” (https://secure-web.cisco.com/1UgnQVFBMbbUsDXUzai5AvAOzqeQ34tRV2D60a4CwFPoV9E...). Cortical reconstruction of the T1 structural image was done in Freesurfer and NODDI processing using the NODDI toolbox in Matlab. The final steps I am attempting to complete include (1) projecting the ODI/NDI maps to an inflated surface to create surface maps (2. Materials and Methods, 2.5 Diffusion-weighted MRI processing); and (2) calculating mean ODI/NDI values across both hemispheres for a selected number of ROIs from the Desikan parcellation (2. Materials and Methods, 2.6 Cortical ROIs). The Parker et al. paper has provided the Freesurfer functions used in each of these final steps, but I am getting stuck on step (2) and am now worried that I have made an error in step (1). Below is the code I have written so far to project an ODI map onto an inflated surface:
bbregister \
--s freesurfer \
--mov odi.nii \
--init-fsl \
--reg register.dat \
--dti
tkregister2 \
--s freesurfer \
--mov odi.nii \
--reg register.dat \
--surf
mri_vol2surf \
--src odi.nii \
--out odi_in_cortex.nativespace.mgh \
--srcreg register.dat \
--hemi lh \
--projfrac 0.5
When I load lh.inflated, the lh.aparc.DKTatlas.annot annotation file, and the odi_in_cortex.nativespace.mgh overlay in Freeview, things seem to be correct. The issue I have is when I try to use mris_anatomical_stats(). I have tried different combinations of label and annotation files but am either getting errors or no errors but also no output. Any guidance would be much appreciated! I am new to Freesurfer and have been learning it as part of my graduate research assistantship. I am using Freesurfer version 7.1.1 on a macOS Catalina, version 10.15.7 operating system for reference. Cheers, Alexandria Jensen