Hi Doug, There is a bit of movement across the 3 acquisitions. How may I align everything together before running mri_concat?
1. Run bbregister or mri_coreg to register 1 acquisition to T1 2. Use the reg file to move the remaining 2 acquisitions ? Is there a quicker way? Thank you. -- Shane Schofield On 9 March 2017 at 17:01:28, Douglas N Greve (gr...@nmr.mgh.harvard.edu) wrote: If the 3 volumes are in register (ie, no motion between them), then I would just run the mri_concat command to create a single volume which is the average of the 3, then proceed as described. On 03/09/2017 11:58 AM, Shane S wrote: > Hi Doug, > > I want to derive a single averaged PET volume from the three > reconstructed 5 min acquisitions, expressed in detected counts. Then > we will divide the counts based on the cerebellum. Following that, I > want to use PetSurfer for partial volume correction and GLM > comparisons. May I upload the 3 images per subject? > > Thank you. > > -- > Shane S > > On 9 March 2017 at 16:18:33, Douglas N Greve > (gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>) wrote: > >> How are you planning on analyzing the different time points? >> >> >> On 03/08/2017 05:33 PM, Shane S wrote: >> > Dear Doug, >> > >> > My PET data is 3 x 5 minute acquisitions. Each subject has >> > subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz and I am >> > supposed to align and average them. >> > >> > Please advise. >> > >> > Thanks! >> > >> > -- >> > Shane Schofield >> > >> > On 8 March 2017 at 22:31:06, Douglas Greve (gr...@nmr.mgh.harvard.edu >> > <mailto:gr...@nmr.mgh.harvard.edu>) wrote: >> > >> >> No, the template is a within subject template used for registration. >> >> If your pet data only has one frame (eg, FDG SUV), then you don't >> >> need to run mri_convert or mri_concat, just use your pet image as the >> >> template >> >> >> >> >> >> On 3/8/17 11:11 AM, Shane S wrote: >> >>> Hello Freesurfer, >> >>> >> >>> I have 3 PET images per individual. I am learning PetSurfer based on >> >>> the Greve et al., 2014 paper. >> >>> >> >>> On the PetSurfer link, there are 2 methods. >> >>> >> >>> mri_convert pet.nii.gz —frame frameno template.nii.gz >> >>> or >> >>> mri_concat pet.nii.gz --mean —0 template.nii.gz >> >>> >> >>> What are the differences? My files are listed as >> >>> subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz >> >>> >> >>> Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz, >> >>> subject123_c.nii.gz —mean —o template.nii.gz” correct? >> >>> >> >>> Thank you for helping. >> >>> >> >>> Best Wishes, >> >>> >> >>> S >> >>> -- >> >>> Shane Schofield >> >>> >> >>> >> >>> _______________________________________________ >> >>> 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 >> >> >> >> >> >> 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. >> > >> > >> > _______________________________________________ >> > 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 -- 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
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