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

<mailto:greve@nmr.mgh.harvard.edu
<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 Greve
<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>>>> 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
<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>>>>> 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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