Dear Freesurfers,
I am trying to implement
the methods mentioned in this paper to deal with partial
volume effects when quantifying metabolites: https://www.ncbi.
The first step it mentions is: A binary mask must first be created, which represents the 3D SVS voxel. A binary mask is an image where each voxel contains either 1 or 0; in this case, the SVS voxel would be represented by a value of 1 and all other voxels 0. There are multiple ways to create a binary mask; one example, which was used successfully in this work, is the “mask()” function within Matlab9 and the FreeSurfer (Fischl)10 application “mri_volsynth.”
When I am trying the following command in FreeSurfer:
mri_volsynth --dim 3 4 5 2 --vol try.IMA
I am getting this output:
But, I
don’t know where it is saving the output file. And, I am also
not sure whether I am using mri_volsynth correctly. What is
--dim nc nr ns nf in https://surfer.nmr.mgh.
Also which pixels suppose to be 1's
and which 0's?
Any help is appreciated.
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