1 Nov
2016
1 Nov
'16
5:58 p.m.
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 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> 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 > <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 thecross
> 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>>> wrote: >> >> It would depend on how big the ROI is to begin with. Doyou
>> know that we >> have our own interhemispheric analysis that might bebetter
>> 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 >> > <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 biasthings,
>> 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 ofeach
>> 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 toyou
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