Hi Mahmoud,

I haven't done this so maybe it's wrong, other should know better.

freesurfer uses 256 cube resolution for their voxel space. RAS coordinates are not changed and everything is stored in file headers. Unless bet changes header information, the images should still be on top of each other (in RAS coordinates). Probably fslview cannot read the header correctly?
Try freeview for loading both images.

You can also try to reslice the brainmask.mgz like the other image (but that means applying interpolation wich is not what you may want to do).

mri_convert -rl test_brain.nii -rt nearest /xxx/mri/brainmask.mgz /xxx/test_brainmask.nii.gz
(using nearest neighbor interpolation).
Or map the FSl image to freesurfers voxel space.

Best, Martin

On 10/24/2014 11:34 AM, Mahmoud wrote:

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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-- 
Dr. Martin Reuter

Instructor in Neurology
  Harvard Medical School
Assistant in Neuroscience
  Dept. of Radiology, Massachusetts General Hospital
  Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
  Computer Science and Artificial Intelligence Lab,
  Dept. of Electrical Engineering and Computer Science,
  Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email: 
   mreuter@nmr.mgh.harvard.edu
   reuter@mit.edu
Web  : http://reuter.mit.edu 

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