Hello all,
We would like to analyise our repeated measures DTI data using an ANOVA. We are wondering if someone might have experience running AVOVA's on 3D data? Is there a particular tool used or did you use MATLAB for this type of analysis?
Thank you,
Sandra
Sandra Woodman Mood and Motor Control Laboratory Athinoula Martinos Center for Biomedical Imaging Massachusetts General Hospital
Hi Sandra, it is usually just a matter of setting up a design matrix and contrast matrices to test what you are interested in then using any glm software. If you just have two time points, then you can just subtract them and do a one-sample group mean (design matrix a column of all ones; contrast matrix = [1]).
doug
swoodman@nmr.mgh.harvard.edu wrote:
Hello all,
We would like to analyise our repeated measures DTI data using an ANOVA. We are wondering if someone might have experience running AVOVA's on 3D data? Is there a particular tool used or did you use MATLAB for this type of analysis?
Thank you,
Sandra
Sandra Woodman Mood and Motor Control Laboratory Athinoula Martinos Center for Biomedical Imaging Massachusetts General Hospital
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Freesurfers,
I am ready to run the make_average_subject and I need to specify -xform for the talairach transform: talairach.lta , talairach.m3z or talairach.xfm. What is the difference between this and what should I use for the make_average_subject in order to prepare my data for the GLM analysis?
Thank you very much for your help. Antonella
Hi Antonella
talairach.lta and .xfm are linear transforms to a Talairach coordinate system. The .m3z is a nonlinear morph and will give you much higher anatomical resolution.
cheers Bruce
On Thu, 11 Aug 2011, Antonella Kis wrote:
Dear Freesurfers,
I am ready to run the make_average_subject and I need to specify -xform for the talairach transform: talairach.lta , talairach.m3z or talairach.xfm. What is the difference between this and what should I use for the make_average_subject in order to prepare my data for the GLM analysis?
Thank you very much for your help. Antonella
Hi Bruce,
Many thanks again for your help. So just to make sure that I understood corect: is better to use the talairach.m3z win my make_average_subject? I was reading that the talairach coordinate is based on talairach.xfm (unless changed with --xform) so your suggestion was to change it to talairach.m3z?
Many thanks. Antonella
________________________________ From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, August 11, 2011 12:52 PM Subject: Re: [Freesurfer] (no subject)
Hi Antonella
talairach.lta and .xfm are linear transforms to a Talairach coordinate system. The .m3z is a nonlinear morph and will give you much higher anatomical resolution.
cheers Bruce
On Thu, 11 Aug 2011, Antonella Kis wrote:
Dear Freesurfers,
I am ready to run the make_average_subject and I need to specify -xform for the talairach transform: talairach.lta , talairach.m3z or talairach.xfm. What is the difference between this and what should I use for the make_average_subject in order to prepare my data for the GLM analysis?
Thank you very much for your help. Antonella
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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.
it depends whether you want things in a coordinate system that is more anatomically accurate (.m3z) or more of a true "Talairach" one (talaraich.xfm)
On Thu, 11 Aug 2011, Antonella Kis wrote:
Hi Bruce,
Many thanks again for your help. So just to make sure that I understood corect: is better to use the talairach.m3z win my make_average_subject? I was reading that the talairach coordinate is based on talairach.xfm (unless changed with --xform) so your suggestion was to change it to talairach.m3z?
Many thanks. Antonella
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, August 11, 2011 12:52 PM Subject: Re: [Freesurfer] (no subject)
Hi Antonella
talairach.lta and .xfm are linear transforms to a Talairach coordinate system. The .m3z is a nonlinear morph and will give you much higher anatomical resolution.
cheers Bruce
On Thu, 11 Aug 2011, Antonella Kis wrote:
Dear Freesurfers,
I am ready to run the make_average_subject and I need to specify -xform for the talairach transform: talairach.lta , talairach.m3z or talairach.xfm. What is the difference between this and what should I use for the make_average_subject in order to prepare my data for the GLM analysis?
Thank you very much for your help. Antonella
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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@nmr.mgh.harvard.edu
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Antonella Kis -
Bruce Fischl -
Douglas N Greve -
swoodman＠nmr.mgh.harvard.edu