That file would be anything you want to rescale. So gtm.nii.gz would be a candidate (as would an Muller-gartner PVCed volumes).
On 02/16/2017 03:32 PM, Anderson Napolitano wrote: > I am so sorry about that Dr. Greve. > The post I made earlier is reference from the following thread: > On 02/16/2017 12:28 PM, Anderson Napolitano wrote: > > > > Thank you Dr. Greve. Just to clarify, the 'inputfile.nii.gz' file in > > the command: > > > > fscalc inputfile.nii.gz div value -o outputfile.nii.gz > > ,is the gtm.nii.gz file generated after the command: > > mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg > > gtmseg.mgz > > --default-seg-merge --auto-mask PSF .01 --mgx .01 --o gtmpvc.output > > located at gtmpvc.output directory? If that's the case, fscalc will > > not modify > > gtm.stats.dat file corresponding to the image. Wouldn't that be > > counter intuitive, > > as gtm.stats.dat remains unchanged but we just normalized the image > > using the > > fscalc command? > > Again, thank you Dr. Greve. I really appreciate all the help. > > -Anderson > >> There is not a flag to do this, but it should be fairly easy. There will > >> be a file called aux/global.gmwmcsf.dat. This has the mean value average > >> over all GM, WM, and CSF voxels (after PVC). You can use this to scale > >> your data like > >> fscalc inputfile.nii.gz div value -o outputfile.nii.gz > >> You can also use the --scale option when running mri_vol2surf to apply a > >> scaling factor when projecting on to the surface > > On 02/14/2017 02:04 PM, Anderson Napolitano wrote: > >>> Hi Experts! > >>> > >>> > >>> Quick question: is it possible to re-scale intensities relative to the > >>> full > >>> brain atlas? > >>> Details: > >>> Per step 3 of the following tutorial: > >>> > >>>https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer > >>> > >>> > >>> I wanted to re-scale the the intensities relative to the full brain > >>> atlas. The > >>> command: > >>> > >>> --no-rescale > >>> > >>> removes scaling relative to the Pons and the command: > >>> > >>> --rescale <Ids> > >>> > >>> rescales the intensities relative to the region determined by Ids. Would > >>> listing all the regions on the --rescale command be the right approach to > >>> rescale the intensities relative to the atlas? If so, how do I determine > >>> which > >>> Ids is which? > >>> > >>> > >>> Thank you in advance! > >>> > >>> > >>> -Anderson > >>> > >>> > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> 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 > >>Phone Number: 617-724-2358 > >>Fax: 617-726-7422 > >> > >>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >>FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 > >>www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >>Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >> > >>_______________________________________________ > >>Freesurfer mailing list > >>Freesurfer@nmr.mgh.harvard.edu > >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > Freesurfer mailing list > 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 Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
