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
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
freesurfer@nmr.mgh.harvard.edu
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Anderson Napolitano -
Douglas N Greve