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