[Freesurfer] How to use mris_register

Hi, all, I am new to FreeSurfer world. I am trying to do the surface-based registration using FreeSurfer. I found a tool called mris_register, which is defined as a command registering a surface to an average surface template(or another single-subject's surface). But I don't understand how to use

Re: [Freesurfer] How to use mris_register

arguments? Thank you again. Best, Xiaojing 2009/10/6 Bruce Fischl > Hi Xiaojing, > > the inputs are an individual subject sphere created with mris_sphere, and > statistics in an atlas coordinate system, usually stored in a tif file that > we supply. > > cheers, > B

Re: [Freesurfer] How to use mris_register

something different? > > doug > > Xiaojing Long wrote: > >> Hi, all, >> I am new to FreeSurfer world. I am trying to do the surface-based >> registration using FreeSurfer. I found a tool called mris_register, >> which is defined as a command registering a surface t

Re: [Freesurfer] How to use mris_register

another, but in our experience using the atlas statistics and the > measures of cross-subject variability stabilizes the whole procedure > > On Tue, 6 Oct 2009, Xiaojing Long wrote: > > Hi, Douglas, >> >> Thank you so much for your help. >> >>

[Freesurfer] Averaging cortical thickness maps

Hi, I have a question regarding how to average cortical thickness maps. I have a dataset with 10 MR brain images and I've run recon-all on each of them. So I've got thickness maps ?h.thickness for each subject. I wonder whether freesurfer provides a tool that can average the cortical thickness ma

Re: [Freesurfer] Averaging cortical thickness maps

the subjects? Thank you. Best, Xiaojing 2010/3/17 Bruce Fischl > Hi Xiaojing, > > mris_average_curvature will do it, and I think Doug has some other tools > that will as well. > > cheers, > Bruce > On Wed, 17 Mar 2010, Xiaojing Long wrote: > > Hi, >> &

Re: [Freesurfer] Averaging cortical thickness maps

I would use -o fsaverage, then you can simply load the average > thickness onto the fsaverage inflated surface. > > cheers > Bruce > > > > On Thu, 18 Mar 2010, Xiaojing Long wrote: > > Hi, Bruce, >> >> Thanks a lot for your suggestion. >> >>

[Freesurfer] How to convert a cortical thickness map to a NIFTY file

Hi, I have a question regarding how to convert a cortical thickness map (i.e. lh.thickness) to a NIFTY file. I have a subject called 'subjid' and I run recon-all on it. So I got the ?h.thickness files. Does freesurfer provide a tool to convert the surface file to a nifty file? I tried using the

[Freesurfer] How to get deformation maps in surface-based registrations

Hi, all, I have a question regarding how to get the deformation map in surface-based registration. I am wanting to use mris_register to align two surfaces. Can I get the deformation maps describing the vertex-to-vertex correspondence? How can I get it? Thanks a lot. Best, Xiaojing _

Re: [Freesurfer] How to get deformation maps in surface-based registrations

tween the ?h.sphere.reg and the > ?h.sphere. I guess you would want to represent them as arcs of great > circles. > > cheers, > Bruce > > On Tue, 18 May 2010, Xiaojing Long wrote: > > Hi, all, >> >> I have a question regarding how to get the deformation map in >>

[Freesurfer] FDR correction in Qdec

Hi, all, I have some questions about performing the FDR correction in Qdec. I ran recon-all on all my subjects, then ran the surface group analysis following the Qdec tutorial. There are 3 factors in the qdec.table.dat file: age, gender and diagnosis. In the Design tab of Qdec, I selected the dis

Re: [Freesurfer] FDR correction in Qdec

I tried that. Still no change. And I tried running Qdec on all of my datasets. The problem occurs on all of them. Xiaojing 2010/7/9 Douglas N Greve > That is strange. Can you change the FDR to something ridiculous like .5 and > see if that changes things? > > Xiaojin

Re: [Freesurfer] FDR correction in Qdec

Now it works if I enter the FDR in the text box -> press Enter -> click on Set Using FDR Thank you so much. Best, Xiaojing 2010/7/9 Douglas N Greve > That is strange. Can you change the FDR to something ridiculous like .5 and > see if that changes things? > > X