It is a little tricky because you don't want to use different masks for
different subjects. I recommend using CVS where I've created a
subcoritcal mask in 2mm space (mri.2mm). So the idea would be that you
map your subcortical MG map to CVS space, then smooth it (mri_fwhm)
specifying the subcor
Dear Dr Greve,
Thank you so much for the quick response.
Just to confirm that I understood the procedure correctly. The analysis is
volume based (i.e. voxel-wise) for the subcortical structures using mask
created by freesurfer's "mri_binarize" for these regions.
Correct?
Original Mess
It is volume-based for subcortical
On 1/12/18 8:17 AM, John Anderson wrote:
Dear Dr Greeve,
I interestingly read the manuscript "Different partial volume
correction methods lead to different conclusions: An (18)F-FDG-PET
study of aging" Thank you for publishing this data.
I understood from
Dear Dr Greeve,
I interestingly read the manuscript "Different partial volume correction
methods lead to different conclusions: An (18)F-FDG-PET study of aging" Thank
you for publishing this data.
I understood from this paper that he recommended stream for PVC is to correct
the PET images using
Hi John
Doug is out of touch for a week. Maybe you can post this again at the end
of next week or early the following if he hasn't responded?
cheers
Bruce
On Fri, 12 Jan 2018, John Anderson
wrote:
Dear Dr Greeve,
I interestingly read the manuscript "Different partial volume correction
m
Dear Dr Greeve,
I interestingly read the manuscript "Different partial volume correction
methods lead to different conclusions: An (18)F-FDG-PET study of aging" Thank
you for publishing this data.
I understood from this paper that he recommended stream for PVC is to correct
the PET images using
I can when I have a beta version! I'm actively working on putting the
programs together into a package. Check back in a month or so.
doug
On 02/08/2014 03:41 PM, Jonathan DuBois wrote:
> Hi Doug,
>
> Thanks for replying. We are currently working on this analysis, is
> there anyway you could
Hi Doug,
Thanks for replying. We are currently working on this analysis, is there
anyway you could provide a beta version of the PVC code?
Thanks,
Jonathan
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Hi Jonathan, it is not possible in 5.3 to do the PVC. This will be part
of the next major release.
doug
On 02/07/2014 03:45 PM, Jonathan DuBois wrote:
> Hi Freesurfer experts,
>
> I have been using freesurfer for surface-based PET analysis and was
> wondering if the method for voxel-based p
Hi Freesurfer experts,
I have been using freesurfer for surface-based PET analysis and was
wondering if the method for voxel-based partial volume correction, used
in the recent paper (Cortical surface-based analysis reduces bias and
variance in kinetic modeling of brain PET data), was implemente
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/s
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
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> you'll need to get a new version then. You won't need to reanalyze
> your anatomicals in
Will I need to re-register the pet to the mri?
On Fri, Jun 10, 2011 at 10:58 AM, Douglas N Greve 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
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
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
>
I'm using 4.4.0
On Fri, Jun 10, 2011 at 10:44 AM, Douglas N Greve 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_c
Hi Corinna,
what version of FS are you using?
Bruce
On Fri, 10 Jun 2011, 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 FreeSur
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
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
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 yo
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?
Also, has anyone published using this pv correction method that you know of?
An alternative method that I was thinking was to do something similar to the
corti
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 p
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 simil
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
c
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