Re: [Freesurfer] Surface based paired t test
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 >> 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 > 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] Surface based paired t test
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 > 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Surface based paired t test
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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Surface based paired t test
Try following this tutorial. It is for fmri, but you can probably apply it to PET surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_freeview Also see you PET module: surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_freeview On 11/20/2018 06:34 PM, john Anderson wrote: > > External Email - Use Caution > > 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 > 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] Surface based paired t test
External Email - Use Caution 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
