1 Nov
2016
1 Nov
'16
6:53 p.m.
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 <greve@nmr.mgh.harvard.edu mailto:greve@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 > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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" > >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 > >> > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@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>>> > >> <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 <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>>> > >> > > >> > <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. 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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 > 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>> > > > > > _______________________________________________ > 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 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>
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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/