New subject: mris_anatomical_stats() for ODI maps inflated to surface

22 Apr 2021

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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” (*MailScanner has detected a possible fraud
  attempt from "secure-web.cisco.com" claiming to be*
  https://onlinelibrary.wiley.com/doi/full/10.1002/hbm.24056
  <https://secure-web.cisco.com/1UgnQVFBMbbUsDXUzai5AvAOzqeQ34tRV2D60a4CwFPoV9ELm-tRW3UuArQKODsri6BLyF4EJHmNa9nKGS6jNCozaQ7DSSoo35W2Zcq8BiNph6IZdeBEPNibwjmOvLYqUKZ0s8CGUz3jDE8YU5aGEgmDYWpSFjTol96_wyLt3oAMNC2yHszucWMRU86DbnyyzXdV62_hUR6rolZPdllR4HqwHp7lR9Fbv7Fa3VEie64eiPeN3xened9Yqs3paID3QvXxY3WNwHWdkUkXhgePXyQ/https%3A%2F%2Fonlinelibrary.wiley.com%2Fdoi%2Ffull%2F10.1002%2Fhbm.24056>).
  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

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