We don't have anything that will read xls format into a surface. From matlab you can save it as a curv or mgh file as I describe below. I think you can run these under windows since they are simply matlab files. You'd need to have access to them on your windows machine, but you can do this by copying $FREESURFER_HOME/matlab and $FREESURFER_HOME/fsfast/toolbox.
doug
Feng-Xian Yan wrote:
Hi,
Thank you for your suggestion. But, I run the MATLAB under windows XP, because I can’t setup the MATLAB under LINUX. I don’t know what’s wrong, and now I only run MATLAB under windows XP.
So, when I did anova command to obtain F value and p value using MATLAB under windows XP. I save these values in xls format. Then, I would like to map F value and p value to inflated surface of fsaverage, respectively.
Could you tell me how to do and what command do I type? And, what’s the functional volume? Thank you in advance!
Feng-Xian Yan
2009/10/1 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
The easiest thing to do is to specify your output of mri_surf2surf as mgh format instead of curv. The read that directly into matlab with our MRIread() matlab command (ie, no mris_convert stage). Make your computations in matlab, then write them out as mgh format using MRIwrite(). doug Feng-Xian Yan wrote: Hi, The mri_surf2surf command line was mris_surf2surf --srcsubject xxx --sval xxx/surf/lh.thickness --sfmt curv --hemi lh --trgsubject fsaverage --tfmt curv --tval fsaverage/surf/lh.xxx.thickness mris_convert –c fsaverage/surf/lh.xxx.thickness fsaverage/surf/lh.white fsaverage/surf/lh.xxx.thickness.asc From these two command lines, I obtained the asc file with the coordinates of 163842 vertices and their thickness value. Then, I did anova analysis to obtain F value and p value using MATLAB. After I obtained the results from MATLAB, I want to map these results to inflated surface of fsaverage. Could you tell me how to do and what command do I type? Or, you could recommend me another way to obtain the same map. Thank you in advance! Feng-Xian 2009/10/1 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>>> what was your mri_surf2surf command line? On Thu, 1 Oct 2009, Feng-Xian Yan wrote: Hi, But the number of vertex I obtain using mri_surf2surf is 65536 each hemisphere. So, how can I do to make the number is closer to 130,000? Thank you in advance! Feng-Xian 2009/10/1 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>>> use mri_surf2surf. And you should have more than 65536 vertices/hemisphere. Usually the # is closer to 130,000 On Thu, 1 Oct 2009, Feng-Xian Yan wrote: Hi, I run all my subjects using recon-all ?subjid xxx ?autorecon-all. I get the cortical thickness value of each vertex (65536 each hemisphere). Then I obtain F value and p value of anova analysis using MATLAB. Now, I want to map the results of anova to fsaverage. Could these values do that? Or, you could recommend me another way to obtain the same map. Thank you in advance! Feng-Xian 2009/10/1 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>>> Hi Feng-Xian have you run recon-all on your anatomical data? What kind of data do you want to map? Is it a functional volume? cheers Bruce On Thu, 1 Oct 2009, Feng-Xian Yan wrote: Hi, I have a problem want to solve. I want to map the data file (.xls or .txt) to fsaverage. What command do I type? Thank you in advance! Feng-Xian ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>