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Dear experts,
I am trying to do PVC on FBB-PET images using the following commands:
" mri_coreg --s s_001 --mov s_001_pet_fbb.nii.gz --reg s_001_pet_fbb.reg.lta
mri_gtmpvc --i s_001_pet_fbb.nii.gz --reg s_001_pet_fbb.reg.lta --psf 6 --seg gtmseg.mgz --rescale 174 --default-seg-merge --auto-mask --mgx .1 --o s_001_pet_fbb "
The problem is that when overlaying the mgx.ctxgm.nii.gz file with the T1.mgz of the corresponding subject, they don't match, since the resulting MG-image is in the space of the original PET (without PVC) instead of in the space of the freesurfer subject.
How can I make the MG image be in the freesurfer's subject space? Where is the error? Thank you very much in advance.
Best regards, Marina
External Email - Use Caution
Hello Mam, I am not replying to your mail, instead I need to know the source where you learn Freesurfer and pre processing of MRI and PET. Please do reply.
On Tue, 17 Jan 2023, 11:16 pm Marina Fernández, < marina.fdez.alvarez@gmail.com> wrote:
External Email - Use CautionDear experts,
I am trying to do PVC on FBB-PET images using the following commands:
" mri_coreg --s s_001 --mov s_001_pet_fbb.nii.gz --reg s_001_pet_fbb.reg.lta
mri_gtmpvc --i s_001_pet_fbb.nii.gz --reg s_001_pet_fbb.reg.lta --psf 6 --seg gtmseg.mgz --rescale 174 --default-seg-merge --auto-mask --mgx .1 --o s_001_pet_fbb "
The problem is that when overlaying the mgx.ctxgm.nii.gz file with the T1.mgz of the corresponding subject, they don't match, since the resulting MG-image is in the space of the original PET (without PVC) instead of in the space of the freesurfer subject.
How can I make the MG image be in the freesurfer's subject space? Where is the error? Thank you very much in advance.
Best regards, Marina _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/152zoYXuZJegdWpqoX3cHHTU57mFy5CqxTItV1uDq3g8AO7... 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1Y2n0Lt7qelLI-6JcOyuLSMDYPYuinaE5gMBud17DDwdaQZ... < https://secure-web.cisco.com/1Y2n0Lt7qelLI-6JcOyuLSMDYPYuinaE5gMBud17DDwdaQZ... .
When you load it into freeview, use the aux/bbpet2anat.lta , eg, freeview orig.mgz aseg.mgz mgx.ctxgm.nii.gz:reg=aux/bbpet2anat.lta
On 1/17/2023 12:46 PM, Marina Fernández wrote:
External Email - Use Caution
Dear experts,
I am trying to do PVC on FBB-PET images using the following commands:
" mri_coreg --s s_001 --mov s_001_pet_fbb.nii.gz --reg s_001_pet_fbb.reg.lta
mri_gtmpvc --i s_001_pet_fbb.nii.gz --reg s_001_pet_fbb.reg.lta --psf 6 --seg gtmseg.mgz --rescale 174 --default-seg-merge --auto-mask --mgx .1 --o s_001_pet_fbb "
The problem is that when overlaying the mgx.ctxgm.nii.gz file with the T1.mgz of the corresponding subject, they don't match, since the resulting MG-image is in the space of the original PET (without PVC) instead of in the space of the freesurfer subject.
How can I make the MG image be in the freesurfer's subject space? Where is the error? Thank you very much in advance.
Best regards, Marina
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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