Dear all, I have a set of T1-MPRAGE images and and conducted the following steps:
1- Converted the DICOM images to SPM8 (3D nifti nii) by dcm2niigui.exe 2- Used the following line to segment images by FreeSurfer: recon-all -i /xxx/IM-0009-0001.dcm -subject TEST -all recon-all -base TESTBASE -tp TEST -all recon-all -long TEST TESTBASE -all 3- Used FSL BET to skull strip the nii file from step 1 and then fed the output into FSL FAST segmentation to segment it to 3 classes. 4- Used the following line to convert the mgz file to nii mri_convert --in_type mgz --out_type nii --out_orientation RAS /xxx/mri/brainmask.mgz /xxx/test_brainmask.nii 5- Using the fslinfo it gives me the following info for test_brain.nii.gz data_type FLOAT32 dim1 192 dim2 240 dim3 256 dim4 1 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 1.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ while for the nii file from step 4 the fslinfo gives me: data_type UINT8 dim1 256 dim2 256 dim3 256 dim4 1 datatype 2 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 2.300000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ As you may see these two files are completly different so I am not able to overlay them using FSLVIEW. Any idea about how to overlay them ? Thank you, Mahmoud
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