Dear FSL Users,
I am trying to register the DTI sequence (FLIRT) to a mprage vol so that we can utilize the mask created from the mprage.
Here is what I did:
1. extract the 3D no-diffusion vol from the DTI sequence(4D). (Both are already skull stripped)
2. register the no-diffusion vol to the mprage and save the transformation matrix:
flirt -in nodiffusion.nii.gz -ref mprage.nii.gz -out NodiffusionRegToMprage.nii.gz -omat NodiffusionRegToMprageMat
3. Align all DTI volumes to the mprage volume using the saved matrix:
flirt -in DTIVol0000.nii.gz -ref mprage.nii.gz -applyxfm -init NodiffusionRegToMprageMat -out
DTIRegToMprageVol0000
4. Then create a new 4D DTI sequence from the registered volumes
fslmerge -a DTIRegToMprage DTIRegToMprageVol*
All steps completed successfully except that the new 4D DTI sequence (DTIRegToMprage) has "bad header info". Could anyone tell me what causes this?
Many Thanks,
Rick
All header info are attached below FYI:
1.Old DTI sequence (4D)
data_type INT16
dim1 128
dim2 128
dim3 66
dim4 65
datatype 4
pixdim1 2.0000000000
pixdim2 2.0000000000
pixdim3 2.0000000000
pixdim4 1.0000000000
cal_max 3915.0000
cal_min 0.0000
file_type NIFTI-1+
2. no-diffusion vol(3D)
data_type INT16
dim1 128
dim2 128
dim3 66
dim4 1
datatype 4
pixdim1 2.0000000000
pixdim2 2.0000000000
pixdim3 2.0000000000
pixdim4 1.0000000000
cal_max 3915.0000
cal_min 0.0000
file_type NIFTI-1+
3.Mprage
data_type FLOAT32
dim1 160
dim2 512
dim3 512
dim4 1
datatype 16
pixdim1 1.0000000000
pixdim2 0.5000000000
pixdim3 0.5000000000
pixdim4 1.0000000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
4.Register no-diffusion vol
data_type INT16
dim1 160
dim2 512
dim3 512
dim4 1
datatype 4
pixdim1 1.0000000000
pixdim2 0.5000000000
pixdim3 0.5000000000
pixdim4 1.0000000000
cal_max 3915.0000
cal_min 0.0000
file_type NIFTI-1+
5.Registered diffusion vols
data_type INT16
dim1 160
dim2 512
dim3 512
dim4 1
datatype 4
pixdim1 1.0000000000
pixdim2 0.5000000000
pixdim3 0.5000000000
pixdim4 1.0000000000
cal_max 3915.0000
cal_min 0.0000
file_type NIFTI-1+
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