Hi Reuben,

On 10/5/2022 10:05 PM, Addison, Reuben wrote:
  1. I am planning to add a seed sphere 6mm cortical and 4 millimeters subcortical and I want to do this with Fsfast using given MNI coordinates from a previous study. I am wondering if there is a command on fsfast to achieve that, I have gone through the connectivity analysis but couldn't quite figure a way to do that.
first look at Case #9 in https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems to convert your MNI152 coordinate to mni305 space
you can then load your orig.mgz into freeview; in the control window, there should be a row that says MNI305. Plug your mni305 coordinate into that to go to that point
In the control window, there will be an orig row with the value of the orig intensity followed by three numbers; these are the col, row, and slice of the point
In a new shell, run
mri_volsynth --template orig.mgz --pdf sphere --sphere-center col row slice --radius RADIUS --o sphere.mgz
Load sphere.mgz with orig.mgz to make sure that it generated the sphere of the proper radius at the proper place

  1.  Also I want to add a covariate (behavioural score) to my second level connectivity map. I want to use fsfast for consistency sake. If I can be pointed to the command it will be very helpful.
Do this in the FSGD file
Thanks, 

Reuben N. Addison

Postdoctoral Fellow 

Brain Recovery Lab

MGH Institute of Health Professions 

Charlestown Navy Yard | 36 1st Avenue, Boston MA 02129



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