It should save it in the current directory. But I don't think we write out IMA files. Why not use nifti (nii or nii.gz)?

On 4/5/17 2:05 PM, Karan Vahi wrote:

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.nlm.nih.gov/pmc/articles/PMC4849426/#__sec2title https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4849426/#__sec2title

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:

Inline image 1

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.harvard.edu/fswiki/mri_volsynth https://surfer.nmr.mgh.harvard.edu/fswiki/mri_volsynth?

Also which pixels suppose to be 1's and which 0's?

Any help is appreciated.

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