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
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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 <mreuter@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 listFreesurfer@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: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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That mri_convert command only changes the file from mgz to nii. If you want to resample it into a new space, then use mri_vol2vol using --regheader doug
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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Mahmoud -
Martin Reuter