did you check the registration? Run mni152reg --help to see how On 2/26/19 2:36 PM, john Anderson wrote: > > External Email - Use Caution > > Hi Dr Greve, > > 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.ande...@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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
