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.
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? Thank you! Daiana On Tue, Nov 1, 2016 at 5:22 PM, Douglas N Greve <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>> 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 > > > > > > 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>>> 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>>> 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>> > > >> > > >> > > >> 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>>>> 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 > > >> > > > >> > > > >> > > > >> > _______________________________________________ > > >> > 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> > > >> <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> > > > <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 > > gr...@nmr.mgh.harvard.edu <mailto:gr...@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:freesur...@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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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