[Freesurfer] ascii file

Hi, I had asked two problems before; one is what is coordinates when I type mris_convert -c lh.thickness lh.white lh.thickness.asc, and another is if the asc file doesn't use Tal coordinate, what commands do I type to obtain the thickness asc with Tal coordinate?, and then you responded me with

Re: [Freesurfer] ascii file

t guessing though. > Doug is the expert on this. > > cheers, > Bruce > > > > On Tue, 4 Aug 2009, Feng-Xian Yan wrote: > > Hi, >> >> I had asked two problems before; one is what is coordinates when I >> type mris_convert >> -c lh.thickness lh.wh

Re: [Freesurfer] ascii file

Hi, I change the input and output from curv to surface, but the error is the same. So, how do I do to resolve it? Thank you in advance! Feng-Xian 2009/8/5 Douglas N Greve > The output is not a curvature file, it is a surface. > > doug > > Feng-Xian Yan wrote: > >

[Freesurfer] thickness map

Hi, I have some problems want to understand. (1) I want to analysis the cortical thickness difference of three groups. But, three groups (one factor/three levels) of Freesurfer is not satisfied with our demand. Because we want to get a thickness difference map that satisfied with the many v

Re: [Freesurfer] thickness map

2009/8/18 Feng-Xian Yan > > Thank s for your response. > > So, the coordinates are MNI coordinates, not Talairach coordinates. > > > > Thank you in advance. > > > > Feng-Xian > > > > 2009/8/18 Douglas N Greve > >> The values in the asc

Re: [Freesurfer] thickness map

tools do. You can find tutorials > on the wiki. You'll probably start with mris_preproc. > > doug > > > > > On Thu, 20 Aug 2009, Feng-Xian Yan wrote: > > Hi, >> >> Thank you for your responses before. >> >> >> >> I have anoth

[Freesurfer] vertex number

Hi, I know Freesurfer has a function which can label ROI by us. But, I want to know how many vertices do the labeled ROI has. Would you teach me how to obtain the vertex of the labeled ROI ? Thank you in advance! Feng-Xian ___ Freesurfer mailin

Re: [Freesurfer] thickness map

2009/8/25 Feng-Xian Yan > Hi, > >First, I use mri_surf2surf (as follows) to map our subjects to > fsaverage. > > mri_surf2surf –srcsubject subject --sval-tal-xyz white --hemi lh > --trgsubject fsaverage --tval-xyz --tval lh.subject.tal > > > > Next ste

[Freesurfer] map .xls or .txt file to fsaverage

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 https://mail.nmr.mgh.harvard.edu/mailma

Re: [Freesurfer] map .xls or .txt file to fsaverage

> > 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-Xia

Re: [Freesurfer] map .xls or .txt file to fsaverage

sually 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 >> ob

Re: [Freesurfer] map .xls or .txt file to fsaverage

in the same space? > > Bruce Fischl wrote: > >> 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, >>> >>&g

Re: [Freesurfer] map .xls or .txt file to fsaverage

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 > what was your mri_surf2surf command line? > > On Thu, 1 Oct 2009, Feng-Xian Yan w

Re: [Freesurfer] map .xls or .txt file to fsaverage

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 > The easiest th

[Freesurfer] convert inflated surface to mnc

Hi, Thank you for your responses before. Now, I want to convert the inflated surface of fsaverage to the .mnc file which file I want to do the template for spm. What command do I type to obtain .mnc file? Thank you in advance! Feng-Xian ___ Freesurfe

Re: [Freesurfer] problems

Hi, Pedro Paulo Oliveira: Thank you for your answers. But, I'm a rookie of Linux. I don't know what do you mean and how to do that for the answer 2? Can you tell me detail and get me some command lines? Thank you again. 2007/10/4, Pedro Paulo Oliveira Jr <[EMAIL PROTECTED]>: > 1) Yes. mri

[Freesurfer] equipment

Hi, I want to use freesurfer to quantity cortical thickness, and I want to use the software under Linux fedora core 4. What equipment for computer do you recommend? Think you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.

[Freesurfer] version

Hi, I want to use freesurfer to quantify cortical thickness, and I want to use the software under Linux fedora core 4. My computer's equipment is Quad-Core processor Intel Q6600, DDR2 memory 4GB, Sata2 disks 320G, GeFORCE8600. Which version do you recommend? i386? or x86_84? Thanks __

Re: [Freesurfer] problems

Hi, I do that you type, but it is also error. And, I find "libstdc++.so.6", not"libstd++.so.6". What is difference between them? And, what can I do next?? Iteration 1 Thu Dec 13 11:49:43 CST 2007 nu_correct -clobber ./tmp.mri_nu_correct.mni.4568/nu0.mnc ./tmp.mri_nu_correct.mni.4568/nu1.mnc [EMA

[Freesurfer] checking problems

Hi, I have some confusion. When I completely run the command, recon-all –s x249 –autorecon1, and I should stop to check for problems with intensity normalization, talairach transformation and skull stripping. How can I do to check these problems? And, which is I must do first? Thanks. _

[Freesurfer] which image is the best

Hi, I have a problem about which image is the best to run. I had ran the 1.5T data in freesurfer. Because the contrast of the 1.5T data was too bad, I use the 3T data and rerun again. When I run, it says the warning, WARNING The phys

[Freesurfer] qdec

hi, I have a problem. I analysis my data using qdec. But, after runing the command (recon-all -s subject1 -qcache) I can't find the qdec.table.dat and the discrete factor files. The following commands that I type to run. First, I set SUBJECTS_DIR to a directory. setenv SUBJECTS_DIR $SUBJECTS_DIR

[Freesurfer] cortical thickness

Hi, I have some questions about cortical thickness. What method does freesurfer calculate the cortical thickness? Can freesurfer provide the cortical thickness value at each voxel in the gray matter? Thank you in advance. Feng-Xian ___ Freesurfer mail

[Freesurfer] cortical thickness

Hi, After I ran the qdec and analyzed my data(cortical thickness). I have two questions. First, after I display a plot of the data for a particular vertex by left-clicking on a point while holding down the Ctrl key, it shows a plot and its plot window shows this vertex's surface coordinates. Wh

[Freesurfer] Talairach coordinates

Hi, I have some problems about surface coordinates. After running the qdec and analyzed my data(cortical thickness), I display a plot of the data for a particular vertex by left-clicking on a point while holding down the Ctrl key. It shows a plot and its plot window shows this vertex's *surface coo