Re: [Freesurfer] pet partial volume correction

A couple of things: Map aparc+aseg into the PET space: mri_label2vol --seg aparc+aseg.mgz --reg register.dat --temp subject.pet.pvf.nii --o subject_bl.petlabel.nii

Use the PET space aparc+aseg when computing the seg stats: mri_segstats --seg subject_bl.petlabel.nii --sum /home/corinna/blstats/subject.pvcorr.segstats.csv --i subject_bl.petlabel.nii --ctab segments.txt

doug

corinna bauer wrote:

Hi Doug, I tried the partial volume correction method over the weekend and got some unexpected results. Many cortical GM regions were reported as having 0 uptake, left and right hemisphere uptake values for the same ROI were drastically different (i.e. 7 vs 150). Below is my code. Maybe I'm missing something?

mri_compute_volume_fractions register.dat bl_pet.nii subject_bl.pvf fscalc --o subject.pet.pvf.nii bl_pet.nii div subject_bl.pvf.gm.mgz mri_label2vol --seg aparc+aseg.mgz --reg register.dat --temp orig.mgz --o subject_bl.petlabel.nii mri_segstats --seg aparc+aseg.mgz --sum /home/corinna/blstats/subject.pvcorr.segstats.csv --i subject_bl.petlabel.nii --ctab segments.txt

Corinna

On Fri, Jun 10, 2011 at 11:18 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

No, that will be fine.
doug

corinna bauer wrote:

    Will I need to re-register the pet to the mri?

    On Fri, Jun 10, 2011 at 10:58 AM, Douglas N Greve
    <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>> wrote:

       you'll need to get a new version then. You won't need to
    reanalyze
       your anatomicals in the new version, but you will need it
    to run
       these programs.

       doug

       corinna bauer wrote:

           I'm using 4.4.0

           On Fri, Jun 10, 2011 at 10:44 AM, Douglas N Greve
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    <mailto:greve@nmr.mgh.harvard.edu>>>> wrote:


              which version are you using? Both should be in both
    5.0 and
           5.1.
              doug

              corinna bauer wrote:

                  Hi Doug,

                  I used the mri_compute_volume_fractions and
    fscalc commands
                  and got this error message:

                  mri_compute_volume_fractions: Command not found.
                  fscalc: Command not found.

                  Other FreeSurfer commands, such as mri_segstats
    are working
                  fine in the same batch script.

                  Corinna


                  On Wed, Jun 8, 2011 at 2:30 PM, Douglas N Greve
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    <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote:



                     corinna bauer wrote:

                         Alright that should work. So do I use the
           pet.anat.nii
                  files
                         (from mri_vol2vol) as the input pet file
    to the
                         mri_compute_volume_fractions?

                     No, use the pet volume. This does everything
    in the
           pet space.

                         Also, has anyone published using this pv
           correction method
                         that you know of?

                     I don't know. I think this is how they do pvc in
           pet, but I
                  really
                     don't know the lit.


                         An alternative method that I was thinking
    was to do
                  something
                         similar to the cortical thickness correction
           Salat used and
                         sample on either side of the gray/white
    boundary
           and the
                         gray/csf boundary and calculate the ratio. Do
           you think
                  this
                         could account for the effects of pv in pet?

                     David's method was not for doing pvc, and I would
           not use
                  it for pet.

                     doug


                         Corinna


                         On Wed, Jun 8, 2011 at 1:44 PM, Douglas N
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           <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>>>>> wrote:

                            Actually, I think it only will affect
    the volume
                         measurement for
                            each structure, so that's no good.
    There is not a
                  flag to
                            mri_segstats that will do this. If you
    have a
                  registration
                         between
                            your native pet data and the FS anat, then
           you can use

                            mri_compute_volume_fractions regfile.dat
           pet.nii pvf
                            This will create pvf.{gm,wm,csf}.mgz

                            You can then correct the pet with
    something like
                            fscalc pet.nii div pvf.gm.mgz pet.pvf.nii

                            You can map the aparc+aseg into the
    pet space
           using
                         mri_label2vol
                            (and the reg from above), then use
           mri_segstats with the
                         files in
                            the native pet space.

                            doug

                            corinna bauer wrote:

                                Hi Doug,
                                I will give that a try. How will
    this account
                  for the
                         p.v. in
                                pet data? Does it remove the
    voxels that are
                  mixed tissue
                                classes? Does it account for
    partial volume
                  effects between
                                neighbouring grey matter structures?
                                Corinna

                                On Wed, Jun 8, 2011 at 1:06 PM,
    Douglas N
           Greve
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    <mailto:greve@nmr.mgh.harvard.edu>>>>>>> wrote:

                                   Hi Corinna,
                                   try adding --pv mri/norm.mgz
                                   doug

                                   corinna bauer wrote:

                                       Hi all,
                                       I am wondering if partial
    volume
           is taken
                  into
                         account when
                                       calculating average uptake
    values
           of pet
                  data. I
                         know that
                                       aseg.stats takes partial
    volume into
                  account and
                         I am
                                       wondering if there is something
           similar
                  in place for
                                pet data?
                                       From what I gather, most people
           when using
                         FreeSurfer
                                correct
                                       for partial volume effects by
           regressing out
                         cortical
                                       thickness, but no basis for
    this
           correction
                         method has been
                                       provided. Any insight would be
           appreciated.

                                       n.b. to obtain the pet uptake
           values I used
                                mri_segstats --seg
                                       mri/aparc+aseg.mgz --sum
           pet.segstats.dat --i
                         $petanat
                                --ctab
                                       rois.txt

                                       Thank you,
                                       Corinna

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                                <tel:617-726-7422
    <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>
           <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422
    <tel:617-726-7422>>>
                  <tel:617-726-7422 <tel:617-726-7422>
    <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422
    <tel:617-726-7422>
           <tel:617-726-7422 <tel:617-726-7422>>>>>
                                   <tel:617-726-7422
    <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>
           <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422
    <tel:617-726-7422>>>
                  <tel:617-726-7422 <tel:617-726-7422>
    <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422
    <tel:617-726-7422>
           <tel:617-726-7422 <tel:617-726-7422>>>>
                         <tel:617-726-7422 <tel:617-726-7422>
    <tel:617-726-7422 <tel:617-726-7422>>
           <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422
    <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422>
           <tel:617-726-7422 <tel:617-726-7422>>
                  <tel:617-726-7422 <tel:617-726-7422>
    <tel:617-726-7422 <tel:617-726-7422>>>>>>




                                   Bugs:
                  surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
           <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>

    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>

    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>

    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>

     <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>

                                   FileDrop:

    www.nmr.mgh.harvard.edu/facility/filedrop/index.html
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

     <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

     <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

     <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

     <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>




                                   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
                         Partners
                                   Compliance HelpLine at

     http://www.partners.org/complianceline
           . If the
                         e-mail was
                                sent to
                                   you in error
                                   but does not contain patient
           information, please
                         contact the
                                   sender and properly
                                   dispose of the e-mail.



                            --     Douglas N. Greve, Ph.D.
                            MGH-NMR Center
                            greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
           <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>
                  <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
           <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>>
                         <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
           <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>
                  <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
           <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>>>
                         <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
           <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>
                  <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
           <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>>
                         <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
           <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>
                  <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
           <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>>>>
                            Phone Number: 617-724-2358
    <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>
           <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
    <tel:617-724-2358>>>
                  <tel:617-724-2358 <tel:617-724-2358>
    <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358
    <tel:617-724-2358>
           <tel:617-724-2358 <tel:617-724-2358>>>>
                         <tel:617-724-2358 <tel:617-724-2358>
    <tel:617-724-2358 <tel:617-724-2358>>
           <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
    <tel:617-724-2358>>> <tel:617-724-2358 <tel:617-724-2358>
           <tel:617-724-2358 <tel:617-724-2358>>
                  <tel:617-724-2358 <tel:617-724-2358>
    <tel:617-724-2358 <tel:617-724-2358>>>>> Fax:
           617-726-7422 <tel:617-726-7422> <tel:617-726-7422
    <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422>
           <tel:617-726-7422 <tel:617-726-7422>>>
                         <tel:617-726-7422 <tel:617-726-7422>
    <tel:617-726-7422 <tel:617-726-7422>>
           <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422
    <tel:617-726-7422>>>>
                            <tel:617-726-7422 <tel:617-726-7422>
    <tel:617-726-7422 <tel:617-726-7422>>
           <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422
    <tel:617-726-7422>>>
                  <tel:617-726-7422 <tel:617-726-7422>
    <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422
    <tel:617-726-7422>
           <tel:617-726-7422 <tel:617-726-7422>>>>>

                            Bugs:
           surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
           <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>

    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>

    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>

     <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
                            FileDrop:

    www.nmr.mgh.harvard.edu/facility/filedrop/index.html
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

     <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

     <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

     <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>



                     --     Douglas N. Greve, Ph.D.
                     MGH-NMR Center
                     greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
           <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>
                  <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
           <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>>
                  <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
           <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>
                  <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
           <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>>>
                     Phone Number: 617-724-2358 <tel:617-724-2358>
    <tel:617-724-2358 <tel:617-724-2358>>
           <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
    <tel:617-724-2358>>>
                  <tel:617-724-2358 <tel:617-724-2358>
    <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358
    <tel:617-724-2358>
           <tel:617-724-2358 <tel:617-724-2358>>>> Fax:
    617-726-7422 <tel:617-726-7422> <tel:617-726-7422
    <tel:617-726-7422>>
                  <tel:617-726-7422 <tel:617-726-7422>
    <tel:617-726-7422 <tel:617-726-7422>>>
                     <tel:617-726-7422 <tel:617-726-7422>
    <tel:617-726-7422 <tel:617-726-7422>>
           <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422
    <tel:617-726-7422>>>>

                     Bugs:
    surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
           <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>

    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>

     <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
                     FileDrop:

    www.nmr.mgh.harvard.edu/facility/filedrop/index.html
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

     <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

     <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>



              --     Douglas N. Greve, Ph.D.
              MGH-NMR Center
              greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
           <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>
           <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
           <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>>
              Phone Number: 617-724-2358 <tel:617-724-2358>
    <tel:617-724-2358 <tel:617-724-2358>>
           <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
    <tel:617-724-2358>>> Fax: 617-726-7422 <tel:617-726-7422>
           <tel:617-726-7422 <tel:617-726-7422>>
              <tel:617-726-7422 <tel:617-726-7422>
    <tel:617-726-7422 <tel:617-726-7422>>>

              Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
           <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
              <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
              FileDrop:
           www.nmr.mgh.harvard.edu/facility/filedrop/index.html
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

     <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>



       --     Douglas N. Greve, Ph.D.
       MGH-NMR Center
       greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>
       Phone Number: 617-724-2358 <tel:617-724-2358>
    <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422
    <tel:617-726-7422>
       <tel:617-726-7422 <tel:617-726-7422>>

       Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
       <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
       FileDrop:
    www.nmr.mgh.harvard.edu/facility/filedrop/index.html
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
       <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>



-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422
<tel:617-726-7422>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>