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 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 > <gr...@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 < >>> gr...@nmr.mgh.harvard.edu <mailto:gr...@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 >>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>> <mailto:gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@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 >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> >>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> -- Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu> >>> <mailto:gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@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> >>> >>> >>> >>> >>> 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 >>> gr...@nmr.mgh.harvard.edu <mailto:gr...@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> >>> >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
