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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
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%C2%A0but 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
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.anderso@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
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.anderso@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
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.anderso@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%C2%A0but 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
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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
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.anderso@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
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
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
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.anderso@protonmail.com mailto:John.anderso@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%C2%A0but 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@nmr.mgh.harvard.edu
-
Greve, Douglas N.,Ph.D. -
john Anderson