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Dear Freesurfer experts, I have ten PET frames for every subject in my database. these frames represent specific time during PET acquisition. Due to head motion during acquisition the frames are not fully overlapped on top of each other. I created template represent the mean of the ten frames. I would like to register each low res frame to this low res template. Which tool in Freesurfer is more robust to achieve this goal. Any additional suggestions are highly appreciated Thanks John
mri_coreg is the right one for that job
On 07/03/2018 01:51 PM, John Anderson wrote:
Dear Freesurfer experts,
I have ten PET frames for every subject in my database. these frames represent specific time during PET acquisition. Due to head motion during acquisition the frames are not fully overlapped on top of each other. I created template represent the mean of the ten frames. I would like to register each low res frame to this low res template. Which tool in Freesurfer is more robust to achieve this goal. Any additional suggestions are highly appreciated Thanks John
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Dr Greve, If the individual PET frames are named: frame1.nii frame2.nii, frame3.nii ... .... frame10.nii, and the mean for all the ten frames is "frames_mean.nii"
I ran mri_corg on one of the fames as follows: mri_coreg --mov frame1.nii --ref frames_mean.nii --reg reg.dat.
Do I need to run the same command on every frame, or just apply reg.dat on all the frames. If applying reg.dat on all the frames is the correct procedure. How can I do it?
Your guidance is highly appreciated. John
mri_coreg is the right one for that job
‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On July 3, 2018 1:51 PM, John Anderson John.anderso@protonmail.com wrote:
Dear Freesurfer experts, I have ten PET frames for every subject in my database. these frames represent specific time during PET acquisition. Due to head motion during acquisition the frames are not fully overlapped on top of each other. I created template represent the mean of the ten frames. I would like to register each low res frame to this low res template. Which tool in Freesurfer is more robust to achieve this goal. Any additional suggestions are highly appreciated Thanks John
You have to do it for each frame. Use reg.lta instead of reg.dat. You can apply it with mri_vol2vol --mov frame1.nii --reg reg1.lta --o frame1.reg.nii This will use trilinear interpolation by default, but that is probably ok here.
On 07/03/2018 02:29 PM, John Anderson wrote:
Hi Dr Greve, If the individual PET frames are named: frame1.nii frame2.nii, frame3.nii ... .... frame10.nii, and the mean for all the ten frames is "frames_mean.nii"
I ran mri_corg on one of the fames as follows: mri_coreg --mov frame1.nii --ref frames_mean.nii --reg reg.dat.
Do I need to run the same command on every frame, or just apply reg.dat on all the frames. If applying reg.dat on all the frames is the correct procedure. How can I do it?
Your guidance is highly appreciated. John
mri_coreg is the right one for that job
‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On July 3, 2018 1:51 PM, John Anderson John.anderso@protonmail.com wrote:
Dear Freesurfer experts, I have ten PET frames for every subject in my database. these frames represent specific time during PET acquisition. Due to head motion during acquisition the frames are not fully overlapped on top of each other. I created template represent the mean of the ten frames. I would like to register each low res frame to this low res template. Which tool in Freesurfer is more robust to achieve this goal. Any additional suggestions are highly appreciated Thanks John
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Dear Dr Greve – I am immensely impressed with the results. thank you so much for all of your help!!!
Regards john
You have to do it for each frame. Use reg.lta instead of reg.dat. You can apply it with mri_vol2vol --mov frame1.nii --reg reg1.lta --o frame1.reg.nii This will use trilinear interpolation by default, but that is probably ok here.
‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On July 3, 2018 2:29 PM, John Anderson John.anderso@protonmail.com wrote:
Hi Dr Greve, If the individual PET frames are named: frame1.nii frame2.nii, frame3.nii ... .... frame10.nii, and the mean for all the ten frames is "frames_mean.nii"
I ran mri_corg on one of the fames as follows: mri_coreg --mov frame1.nii --ref frames_mean.nii --reg reg.dat.
Do I need to run the same command on every frame, or just apply reg.dat on all the frames. If applying reg.dat on all the frames is the correct procedure. How can I do it?
Your guidance is highly appreciated. John
mri_coreg is the right one for that job
‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On July 3, 2018 1:51 PM, John Anderson John.anderso@protonmail.com wrote:
Dear Freesurfer experts, I have ten PET frames for every subject in my database. these frames represent specific time during PET acquisition. Due to head motion during acquisition the frames are not fully overlapped on top of each other. I created template represent the mean of the ten frames. I would like to register each low res frame to this low res template. Which tool in Freesurfer is more robust to achieve this goal. Any additional suggestions are highly appreciated Thanks John
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
John Anderson