On 11/01/2016 05:58 PM, Daya P wrote:
> Hi,
>
> I have gotten the lh and rh ROIs stats with mris_anatomical_stats 
> before, is there any statistical tests in particular that you 
> recommend for asymmetry? What I have done is a two-way anova and 
> paired t-test with Bonferroni correction. Would like to hear your 
> opinion on that.
That sounds about right. A lot of people will do a laterality index 
(L-R)/(L+R)
>
> Also, I would be interested in the vertex-wise analysis, I will look 
> into that. How can I do the xhemi analysis after make_folding_atlas?
Just follow the instructions on the xhemi page
>
> Thank you!
> Daiana
>
> On Tue, Nov 1, 2016 at 5:22 PM, Douglas N Greve 
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>     You can certainly get the lh and rh ROI stats in table form and
>     then do
>     an asymmetry analysis. Or you can use the xhemi stream to do a
>     vertex-wise analysis. the difference is the difference between ROI and
>     map-based analysis
>
>
>     On 11/01/2016 03:47 PM, Daya P wrote:
>     > Thank you a lot!
>     >
>     > I will try this. I had another question regarding statistical
>     analysis
>     > for asymmetry. I have seen several papers that take the measures
>     that
>     > come from freesurfer (i.e. cortical thickness of auditory
>     cortex), and
>     > use MATLAB or SPSS to run statistical tests.
>     >
>     > I am looking at 13 regions in each hemisphere and want to check for
>     > asymmetry across 9 participants. Is there a way to do this within
>     > Freesurfer?
>     > Otherwise, I am still looking into what the most appropriate
>     test and
>     > post hoc test would be. From asking several people there doesn't
>     seem
>     > to be a straight answer.
>     >
>     > Thank you,
>     > Daiana
>     >
>     > On Tue, Nov 1, 2016 at 12:51 PM, Douglas N Greve
>     > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>     <mailto:gr...@nmr.mgh.harvard.edu
>     <mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
>     >
>     >     I've written a script that will come out with version 6, but
>     I've
>     >     put it
>     >     here
>     >
>     >
>     https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas
>     <https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas>
>     >   
>      <https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas
>     <https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas>>
>     >
>     >     I think it should work in 5.3, but I'm not sure. If not, you can
>     >     download the dev version and make the atlas using that. Run
>     it with
>     >     --help to get info on how to run it.
>     >
>     >
>     >
>     >     On 10/28/2016 05:10 PM, Daya P wrote:
>     >     > Hi Doug,
>     >     >
>     >     > I needed to make a registration template and an cortical atlas
>     >     because
>     >     > I am trying to measure cortical thickness, GM and surface area
>     >     on cat
>     >     > brains.
>     >     >
>     >     > What would be the necessary changes?
>     >     > Would it be possible (and appropriate) to use just
>     >     > mris_left_right_register instead?
>     >     >
>     >     > Daiana
>     >     >
>     >     > On Fri, Oct 28, 2016 at 11:34 AM, Douglas Greve
>     >     > <gr...@nmr.mgh.harvard.edu
>     <mailto:gr...@nmr.mgh.harvard.edu>
>     <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
>     >     <mailto:gr...@nmr.mgh.harvard.edu
>     <mailto:gr...@nmr.mgh.harvard.edu>
>     >     <mailto:gr...@nmr.mgh.harvard.edu 
> <mailto:gr...@nmr.mgh.harvard.edu>>>> wrote:
>     >     >
>     >     >     A difference of 10 out of 500 or 1000 does not both me at
>     >     all. Why
>     >     >     do you need to create your own atlas? It is doable for
>     the cross
>     >     >     hemi stuff, it is just difficult.
>     >     >
>     >     >
>     >     >     On 10/26/16 10:16 AM, Daya P wrote:
>     >     >>
>     >     >>     Thank you for your help!
>     >     >>
>     >     >>     I created a registration template and atlas from scratch
>     >     could I
>     >     >>     input that in the interhemispheric registration analysis?
>     >     >>
>     >     >>     The ROIs for the diffrerent regions per hemisphere
>     are 50-100
>     >     >>     vertices
>     >     >>
>     >     >>     On Oct 24, 2016 5:03 PM, "Douglas N Greve"
>     >     >>     <gr...@nmr.mgh.harvard.edu
>     <mailto:gr...@nmr.mgh.harvard.edu>
>     >     <mailto:gr...@nmr.mgh.harvard.edu
>     <mailto:gr...@nmr.mgh.harvard.edu>>
>     >     <mailto:gr...@nmr.mgh.harvard.edu
>     <mailto:gr...@nmr.mgh.harvard.edu>
>     >     <mailto:gr...@nmr.mgh.harvard.edu
>     <mailto:gr...@nmr.mgh.harvard.edu>>>> wrote:
>     >     >>
>     >     >>         It would depend on how big the ROI is to begin
>     with. Do you
>     >     >>         know that we
>     >     >>         have our own interhemispheric analysis that might
>     be better
>     >     >>         for this?
>     >     >>         Check out
>     >     >>
>     >     >> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
>     <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi>
>     >     <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
>     <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi>>
>     >     >>         <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
>     <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi>
>     >     <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
>     <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi>>>
>     >     >>
>     >     >>
>     >     >>         On 10/24/2016 12:33 PM, Daya P wrote:
>     >     >>         > Hi Bruce,
>     >     >>         >
>     >     >>         > I drew ROIs on an initial subject and then after
>     >     >>         registering all other
>     >     >>         > subjects to the initial one, used
>     mri_label2label to map
>     >     >>         the ROIs from
>     >     >>         > the initial subject to subsequent ones.
>     >     >>         > I am interested in looking at asymmetry between
>     left and
>     >     >>         right regions.
>     >     >>         >
>     >     >>         > I had two concerns, one that the ROIs have
>     different #
>     >     >>         vertices on
>     >     >>         > different subjects, but as you mentioned the
>     nonlinear
>     >     >>         process makes
>     >     >>         > sense, since each subject does not have the
>     exact same
>     >     >>         brain size and
>     >     >>         > curvature.
>     >     >>         >
>     >     >>         > Another concern was that the ROIs on the left
>     and right
>     >     >>         hemisphere in
>     >     >>         > a subject do not have the exact same number of
>     vertices.
>     >     >>         Would a
>     >     >>         > difference of 10 vertices max bias results?
>     >     >>         >
>     >     >>         > Thank you for your help,
>     >     >>         >
>     >     >>         > Daiana R. Pur
>     >     >>         > Research Assistant
>     >     >>         > Canadian Surgical Technologies & Advanced Robotics
>     >     >>         > Brain and Mind Institute
>     >     >>         > Western University
>     >     >>         > London, ON, N6A 5B7
>     >     >>         > Canada
>     >     >>         >
>     >     >>         > On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl
>     >     >>         > <fis...@nmr.mgh.harvard.edu
>     <mailto:fis...@nmr.mgh.harvard.edu>
>     >     <mailto:fis...@nmr.mgh.harvard.edu
>     <mailto:fis...@nmr.mgh.harvard.edu>>
>     >     >>         <mailto:fis...@nmr.mgh.harvard.edu
>     <mailto:fis...@nmr.mgh.harvard.edu>
>     >     <mailto:fis...@nmr.mgh.harvard.edu
>     <mailto:fis...@nmr.mgh.harvard.edu>>>
>     >     >>         <mailto:fis...@nmr.mgh.harvard.edu
>     <mailto:fis...@nmr.mgh.harvard.edu>
>     >     <mailto:fis...@nmr.mgh.harvard.edu
>     <mailto:fis...@nmr.mgh.harvard.edu>>
>     >     >>         <mailto:fis...@nmr.mgh.harvard.edu
>     <mailto:fis...@nmr.mgh.harvard.edu>
>     >     <mailto:fis...@nmr.mgh.harvard.edu
>     <mailto:fis...@nmr.mgh.harvard.edu>>>>> wrote:
>     >     >>         >
>     >     >>         >     Hi Daiana
>     >     >>         >
>     >     >>         >     yes, that is to be expected given the nonlinear
>     >     nature
>     >     >>         of the
>     >     >>         >     cross-subject registration. It shouldn't
>     bias things,
>     >     >>         although
>     >     >>         >     you'll need to give us more details if you
>     want a
>     >     more
>     >     >>         definitive
>     >     >>         >     answer.
>     >     >>         >
>     >     >>         >     cheers
>     >     >>         >     Bruce
>     >     >>         >
>     >     >>         >
>     >     >>         >
>     >     >>         >     On Mon, 24 Oct 2016, Daya P wrote:
>     >     >>         >
>     >     >>         >         Hi All,
>     >     >>         >
>     >     >>         >         My question is about using
>     mri_label2label. When
>     >     >>         mapping the
>     >     >>         >         labels from one
>     >     >>         >         subject to another the number of
>     vertices of each
>     >     >>         ROI is
>     >     >>         >         different. Is that
>     >     >>         >         something to be expected?
>     >     >>         >
>     >     >>         >         How much of a difference does a number of
>     >     vertices
>     >     >>         of 50
>     >     >>         >         compare to 40 have
>     >     >>         >         on measures like thickness, grey matter and
>     >     surface
>     >     >>         area?
>     >     >>         >
>     >     >>         >         I would really appreciate some help
>     >     >>         >
>     >     >>         >         Thank you,
>     >     >>         >
>     >     >>         >         Daiana R. Pur
>     >     >>         >         Research Assistant
>     >     >>         >         Canadian Surgical Technologies & Advanced
>     >     Robotics
>     >     >>         >         Brain and Mind Institute
>     >     >>         >         Western University
>     >     >>         >         London, ON, N6A 5B7
>     >     >>         >         Canada
>     >     >>         >
>     >     >>         >
>     >     >>         >
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>     >     >>
>     >     >>         --
>     >     >>         Douglas N. Greve, Ph.D.
>     >     >>         MGH-NMR Center
>     >     >> gr...@nmr.mgh.harvard.edu
>     <mailto:gr...@nmr.mgh.harvard.edu>
>     <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
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>     <mailto:gr...@nmr.mgh.harvard.edu>
>     <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>>
>     >     >>         Phone Number:617-724-2358 <tel:617-724-2358> 
> <tel:617-724-2358 <tel:617-724-2358>>
>     >     <tel: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>> <tel:617-726-7422
>     <tel:617-726-7422>
>     >     <tel:617-726-7422 <tel:617-726-7422>>>
>     >     >>
>     >     >>         Bugs:
>     surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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>     <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
>     <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>
>     >     >     _______________________________________________ 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>>
>     >     >     <mailto: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>>
>     >     >
>     >     
>     <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>>
>     >     >     <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>
>     >     <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
>     > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>     <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@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>>
>     >
>     >
>     >
>     >
>     > _______________________________________________
>     > 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
>     gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>     Phone Number: 617-724-2358
>     Fax: 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>
>
>
>
>
> _______________________________________________
> 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/

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