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
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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