Dear experts,
I am new to fMRI and I am working with rat fMRI data. I am performing the preprocessing steps in fsl (FMRIB Software Library) and since it designed for human brain, I must scale up the voxel size of rat brain image by 10.
I know that I probably must work with scl_slope and scl_inter in nifti header and I use fsledithd command to change the scl_slope to 10 (Now it is set to 1). but when I change the scl_slope in nifti header, the image doesn't change ( the voxel size remains unchanged.) and I think I must use fslcreatehd command to make these change to my image but I don't know how to do that. if this procedure is right please tell me how I must do that.
Also, I edit the voxel size directly with fsledithd(edit pixdim1, pixdim2 and pixdim3 instead of scl_slope and scl_inter) and it seems that it works, but, I don't know that it is correct to edit those parameter instead of scl_slope or not.
Thank you.
Dear Laila,
While I am not familiar with these functions in FSL, I have an alternative solution. I do know that AFNI has a simple program that does exactly what you want to achieve. It's called 3dresample:
(https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dresample.html).
The option you would like to use is: -dxyz
Best wishes,
Michal
Dear Michal,
Thank you so much for your suggestion.
I have not installed AFNI on my computer, but 3dresample tool can work for 4d fMRI data as well?
Unfortunately, FSL needs a linear transform file to accomplish such task. Flirt takes these files and in your case an identity matrix with the diagonal parts set to ten.
e.g.:
10 0 0 0
0 10 0 0
0 0 10 0
0 0 0 1
Thank you for your responses,
I found that in FSL we can change niftii header info by using of fsledithd command, and then change the dx, dy, and dz parameters (x10) as well as sto_xyz_matrix.
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