Hi Lauri, yes, that's fine. It should give the same answer since you are
not using PVC or accounting for TFE.
doug
On 3/26/2025 11:14 AM, Lauri Tuominen wrote:
External Email - Use Caution
Dear PETsurfers,
I am trying to use PETsurfer and MRTM2 to analyze a SynVesT1 PET scan
with centrum semiovale as a reference region. I have created a
binary mask for centrum semiovale.
I guess my issue is that I don't understand what mri_gtmpvc does if I
don't want to do partial volume correction.
So my question is if it's ok to extract the time series from the
reference region using eg. mri_segstats and use it in the subsequent
commands something like so:
```
mri_gtmpvc --i ${pet_dir}/mc_${pet_file} --reg
${pet_dir}/p2mri.reg.lta --seg gtmseg.mgz \
--default-seg-merge --auto-mask 1.01 --no-tfe --o
${pet_dir}/gtmpvc_hb.output \
--km-hb 11 12 13 50 51 52 --no-rescale --max-threads-minus-1
mri_segstats --i ${pet_dir}/mc_${pet_file} --reg
${pet_dir}/p2mri.reg.lta --seg
$SUBJECTS_DIR/test_subject/mri/cs_eroded.nii.gz --id 1 --avgwf
${pet_dir}/ref.km.txt
mri_glmfit --y ${pet_dir}/gtmpvc_hb.output/km.hb.tac.nii.gz --mrtm1
${pet_dir}/ref.km.txt time.dat --o mrtm1 --no-est-fwhm --nii.gz
```
Thank you so much!
Lauri Tuominen
_______________________________________________
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
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://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
