Hello FreeSurfers,
I would like to run a group analysis on cortical thickness using existing Desikan labels.
When I run the command for smoothing, should I replace *--cortex* with *--label-trg*? In other words, for ROI analysis, should we smooth *only* the target mask?
mri_surf2surf --hemi lh \ --s fsaverage \ --sval lh.gender_age.thickness.00.mgh \ --fwhm 10 \ * --cortex* \ --tval lh.gender_age.thickness.10B.mgh
I followed the instructions from here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit http://freesurfer.net/fswiki/mri_surf2surf
Thank you!
Mihaela
yes, that is the right way to do it
On 03/15/2017 01:18 PM, Mihaela Stefan wrote:
Hello FreeSurfers,
I would like to run a group analysis on cortical thickness using existing Desikan labels.
When I run the command for smoothing, should I replace *--cortex* with *--label-trg*? In other words, for ROI analysis, should we smooth *only* the target mask?
mri_surf2surf --hemi lh \ --s fsaverage \ --sval lh.gender_age.thickness.00.mgh \ --fwhm 10 \ *--cortex* \ --tval lh.gender_age.thickness.10B.mgh
I followed the instructions from here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit http://freesurfer.net/fswiki/mri_surf2surf Thank you! Mihaela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Is there a way or reference this smoothing detail in a paper? There are people who believe that the soothing should be done at the whole brain level and then apply the mask (--label), during the GLM analysis.
Thanks again! Mihaela
On Wed, Mar 15, 2017 at 3:12 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
yes, that is the right way to do it
On 03/15/2017 01:18 PM, Mihaela Stefan wrote:
Hello FreeSurfers,
I would like to run a group analysis on cortical thickness using existing Desikan labels.
When I run the command for smoothing, should I replace *--cortex* with *--label-trg*? In other words, for ROI analysis, should we smooth *only* the target mask?
mri_surf2surf --hemi lh \ --s fsaverage \ --sval lh.gender_age.thickness.00.mgh \ --fwhm 10 \ *--cortex* \ --tval lh.gender_age.thickness.10B.mgh
I followed the instructions from here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit http://freesurfer.net/fswiki/mri_surf2surf Thank you! Mihaela
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 greve@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/
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No, there is not. You can do it that way if you want to. The problem is that you then end up with stuff outside of the ROI smoothing into the ROI. Also note that either way, you will need to generate new tables for correction of multiple comparisons (use use permutation)
On 03/15/2017 03:52 PM, Mihaela Stefan wrote:
Is there a way or reference this smoothing detail in a paper? There are people who believe that the soothing should be done at the whole brain level and then apply the mask (--label), during the GLM analysis.
Thanks again! Mihaela
On Wed, Mar 15, 2017 at 3:12 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
yes, that is the right way to do it On 03/15/2017 01:18 PM, Mihaela Stefan wrote: > Hello FreeSurfers, > > I would like to run a group analysis on cortical thickness using > existing Desikan labels. > > When I run the command for smoothing, should I replace *--cortex* with > *--label-trg*? In other words, for ROI analysis, should we smooth > *only* the target mask? > > mri_surf2surf --hemi lh \ > --s fsaverage \ > --sval lh.gender_age.thickness.00.mgh \ > --fwhm 10 \ > *--cortex* \ > --tval lh.gender_age.thickness.10B.mgh > > > I followed the instructions from here: > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI> > https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit <https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit> > http://freesurfer.net/fswiki/mri_surf2surf <http://freesurfer.net/fswiki/mri_surf2surf> > Thank you! > Mihaela > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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.
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I was thinking to use lme_mass_FDR2 to correct for multiple comparisons. Is there a reason not to use it in this case?
Thank you! Mihaela
On Wed, Mar 15, 2017 at 3:55 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
No, there is not. You can do it that way if you want to. The problem is that you then end up with stuff outside of the ROI smoothing into the ROI. Also note that either way, you will need to generate new tables for correction of multiple comparisons (use use permutation)
On 03/15/2017 03:52 PM, Mihaela Stefan wrote:
Is there a way or reference this smoothing detail in a paper? There are people who believe that the soothing should be done at the whole brain level and then apply the mask (--label), during the GLM analysis.
Thanks again! Mihaela
On Wed, Mar 15, 2017 at 3:12 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
yes, that is the right way to do it On 03/15/2017 01:18 PM, Mihaela Stefan wrote: > Hello FreeSurfers, > > I would like to run a group analysis on cortical thickness using > existing Desikan labels. > > When I run the command for smoothing, should I replace *--cortex* with > *--label-trg*? In other words, for ROI analysis, should we smooth > *only* the target mask? > > mri_surf2surf --hemi lh \ > --s fsaverage \ > --sval lh.gender_age.thickness.00.mgh \ > --fwhm 10 \ > *--cortex* \ > --tval lh.gender_age.thickness.10B.mgh > > > I followed the instructions from here: > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI> > https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit <https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit> > http://freesurfer.net/fswiki/mri_surf2surf <http://freesurfer.net/fswiki/mri_surf2surf> > Thank you! > Mihaela > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/
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no, that is fine too
On 03/15/2017 04:49 PM, Mihaela Stefan wrote:
I was thinking to use lme_mass_FDR2 to correct for multiple comparisons. Is there a reason not to use it in this case?
Thank you! Mihaela
On Wed, Mar 15, 2017 at 3:55 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
No, there is not. You can do it that way if you want to. The problem is that you then end up with stuff outside of the ROI smoothing into the ROI. Also note that either way, you will need to generate new tables for correction of multiple comparisons (use use permutation) On 03/15/2017 03:52 PM, Mihaela Stefan wrote: > Is there a way or reference this smoothing detail in a paper? There > are people who believe that the soothing should be done at the whole > brain level and then apply the mask (--label), during the GLM analysis. > > Thanks again! > Mihaela > > On Wed, Mar 15, 2017 at 3:12 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > yes, that is the right way to do it > > > On 03/15/2017 01:18 PM, Mihaela Stefan wrote: > > Hello FreeSurfers, > > > > I would like to run a group analysis on cortical thickness using > > existing Desikan labels. > > > > When I run the command for smoothing, should I replace > *--cortex* with > > *--label-trg*? In other words, for ROI analysis, should we smooth > > *only* the target mask? > > > > mri_surf2surf --hemi lh \ > > --s fsaverage \ > > --sval lh.gender_age.thickness.00.mgh \ > > --fwhm 10 \ > > *--cortex* \ > > --tval lh.gender_age.thickness.10B.mgh > > > > > > I followed the instructions from here: > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>> > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI>> > > https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit <https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit> > <https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit <https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit>> > > http://freesurfer.net/fswiki/mri_surf2surf <http://freesurfer.net/fswiki/mri_surf2surf> > <http://freesurfer.net/fswiki/mri_surf2surf <http://freesurfer.net/fswiki/mri_surf2surf>> > > Thank you! > > Mihaela > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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Mihaela Stefan