Hello FSL experts,

 

I hope this email finds you well.

 

I have been upsampling my original nii images for all my subjects to the following settings:

 

Number of voxels— X: 96 Y: 96 Z: 64

Voxel Size— X: 2.4 Y: 2.4 Z: 2.4

 

However, for one single subject, the resulting upsampled image is cut-off at the top (superiorly) when I view it through fsleyes and other MRI viewing software (I checked the number of voxels/voxel size, and it is the same as mentioned above).

 

The steps I did to complete the upsampling:

 

Opened FSL GUI; selected FLIRT linear registration; Clicked Utils; Selected “Apply FLIRT transform”; clicked “Use Identity transformation”; Selected Based on: ‘Voxel Dimensions’, inserted the above-mentioned values; Uploaded the original DTI nii file to the input and output volume; selected Go.

 

In this link, I’ve enclosed a screenshot of the upsampled image of how the image is cut-off at the top . I also included a screenshot of the original input nii file.

 

I would greatly appreciate your assistance with this matter.

 

Kind regards,

 

Mikaeel

 

Mikaeel Valli, HBSc | PhD Candidate

Research Imaging Centre | Centre for Addiction and Mental Health

Institute of Medical Science | University of Toronto

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