Right, you can't use --fsgd. The FSGD file is used to get a list of subjects, but you have already specified the list with the --iv options. Does it run properly if you remove --fsgd (but keep --paired-diff)?
On 12/06/2018 12:45 PM, john Anderson wrote: > > External Email - Use Caution > > Hi Dr Greve, yes exactly this is what I did. i user mri_corg and I got > the reg.lta file. Then I used mris_preproc with the flag --iv but this > output an error message that the flags --fsgd, paired-diff and --iv > doesn't work together. This is the reason for my question. > > I appreciate any suggestion. > > > If you have not sampled the PET data onto the surface, you will need > to run mri_coreg to create a registration to the anatomical. Then use > can use mris_preproc with the --iv option (listing each subject with a > different --iv). Run mris_preproc with --help to get examples > > > On 12/06/2018 12:31 PM, john Anderson wrote: > > > > > > External Email - Use Caution > > > > > > Hi Dr Greve, > > >> I tried to follow this web page > > >> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis > > >> This tutorial seems to be for cortical thickness data. After sampling > > >> each individual's surface onto the average surface, how can I modify > > >> this command to fit PET data mris_preproc --target fsaverage --hemi > > >> lh \ > > >>--meas thickness --out lh.paired-diff.thickness.mgh \ > > >>--fsgd pairs.fsgd --paired-diff > > >> > > >> > > >> Thanks for any help! > > >> John > > >> > > >> > > >> ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ > > >> On Tuesday, November 20, 2018 6:34 PM, john Anderson > > >> <john.ande...@protonmail.com <mailto:john.ande...@protonmail.com>> > wrote: > > >> > > >>> Dear Freesurfer experts, > > >>> I would like to run surface based paired t test of PET data on > > >>> surface. For every subject I have visit pre treatment and post > > >>> treatment. I tried to follow the instructions here > > >>> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis but the > > >>> toturial seems to be for cortical thickness data. > > >>> How can i modify the command mris_preproc to do paired test of PEt > > >>> data on brain surface > > >>>mris_preproc --target fsaverage --hemi lh \ > > >>>--meas thickness --out lh.paired-diff.thickness.mgh \ > > >>>--fsgd pairs.fsgd --paired-diff > > >>> thanks for any suggestion > > >>> John > > >> > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: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
