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I used --regheader to move PET to T1.

mni152reg in mri_vol2vol as follows:

mri_vol2vol --mov PET.nii.gz --mni152reg --targ $FSL_DIR/data/standaard/MNI152_2mm_brain.nii.gz --o PET_MNI.nii.gz

this command moved PET to MNI but it crop the image and the orientation is not MNI so Ima not sure what I am doing wrong. Any highlights are appreciated.

My understanding is to move PET to MNI, I need to move PET to T1 then move T1 to MNI the merge the two matrices PET2T1 and T12MNI finally apply warp of PET using this merged matrix but I don't know how I can do it in Freesurfer (if correct).

Thanks for any advice.

John

Why did you use --regheader in vol2vol? You will probably need to do a registration (mri_coreg). Did you check the mni152 reg?

On 2/26/19 10:01 AM, john Anderson wrote:

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐

On Tuesday, February 26, 2019 10:01 AM, john Anderson <John.anderso@protonmail.com> wrote:

Dear FS experts,

I would like to move PET image to MNI152. What is the correct command to do so. I tried

mri_vol2vol --mov PET.nii.gz --s subjID --targ $SUBJECTS_DIR/subjID/mri/orig.mga --regheader --o PET_T1.nii.gz

mni152reg --s subjID

then

mri_vol2vol --inv --targ PET_T1.nii.gz --mov $FSL_DIR/data/standard/MNI152_T1_2mm_brain.nii.gz --o PET_T1_2MNI153_2mm.nii.gz --interp nearest --reg $SUBJECTS_DIR/subjID/mri/transforms/reg.mni152.reg.dat

I still not happy with thresults. PET not perfectly moved to MNI.

please are the steps above correct? Can you kindly suggest any ideas to improve PET registration to MNI?

Thanks

John