Dear Martin, Thank you for your advice. Actually I can overlay both outputs from FSL and FreeSurfer on freeview without any extra work or any change but I was wondering how to do it in FSLView.
Best, Mahmoud On Fri, Oct 24, 2014 at 12:10 PM, Martin Reuter <mreu...@nmr.mgh.harvard.edu > wrote: > 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 > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > 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: > mreu...@nmr.mgh.harvard.edu > reu...@mit.edu > Web : http://reuter.mit.edu > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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