Hi, recently, I am trying to extract information from a preprocessed fMRI data (beta image) with a mask file which is transformed from DTI tract image.
The DTI tractography is done in native space by mrtrix3. The fMRI data is normalized to MNI152 template. So I normalized the native DTI image to MNI152 (using ANTs with 2 steps). Finally, I get binary mask of each tract in MNI152 and fMRI data in MNI152. However, the voxel size and dimensions of these two kinds of data are not the same.
When I execute:
mrstats -mask mask.nii fMRI.nii -output mean
I get error: dimension mismatch between mask.nii and fMRI.nii
So I use mrinfo to check two files and find:
Image name: “mask.nii”
Dimensions: 157 x 189 x 136
Voxel size: 1 x 1 x 1
Data strides: [ 1 2 3 ]
Format: NIfTI-1.1
Data type: 64 bit float (little endian)
Intensity scaling: offset = 0, multiplier = 1
Transform: 1 0 -0 -78
0 1 -0 -112
0 0 1 -50
Image name: “fMRI.nii”
Dimensions: 64 x 76 x 64
Voxel size: 3 x 3 x 3
Data strides: [ 1 2 3 ]
Format: NIfTI-1.1
Data type: 32 bit float (little endian)
Intensity scaling: offset = 0, multiplier = 1
Transform: 1 -0 -0 -94.5
-0 1 -0 -130.5
0 0 1 -76.5
I search this problem and find that mrgrid may be a solution.
I tried that:
mrgrid mask.nii regard -template fMRI.nii mask_grid.nii -interp nearest
Then I check the result and fond that the mask_grid.nii overlapped with mask.nii mostly. But their outline is a bit different and the voxel values near the outline are different.
I don’t know is this the appropriate method for this situation?
Or is their any other better methods?
Thanks a lot.