[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

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 fis...@nmr.mgh.harvard.edu what was your mri_surf2surf command line? On Thu, 1 Oct 2009, Feng-Xian Yan

[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

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

that? Or, you could recommend me another way to obtain the same map. Thank you in advance! Feng-Xian 2009/10/1 Bruce Fischl fis...@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

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

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 fis...@nmr.mgh.harvard.edu use mri_surf2surf. And you should have more than 65536

Re: [Freesurfer] thickness map

2009/8/25 Feng-Xian Yan mimigi...@gmail.com 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 step, I use mris_convert to show

[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

Re: [Freesurfer] thickness map

Hi, But I want to obtain the asc file or other files containing the same vertices and with the cortical thickness value and their coordinates in the file. Could some ways to obtain? Thank you in advance! Feng-Xian 2009/8/20 Doug Greve gr...@nmr.mgh.harvard.edu Yes, this is what

Re: [Freesurfer] thickness map

would to obtain the same vertex number. Therefore, have something to do to obtain the same vertex number, i.e. template the cortical thickness at each vertex for each subject on the fsaverage surface, or other methods? How can I do? Would you get me a hand? Thank you in advance! Feng-Xian

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 gr...@nmr.mgh.harvard.edu The output is not a curvature file, it is a surface. doug Feng-Xian Yan wrote: Hi

[Freesurfer] ascii file

“mris_convert -c lh.noise0.5_0_tal.xfm lh.white lh.thickness.asc” But, this has an error: MRISreadBinaryCurvature: incompatible vertex number in file ./lh.noise0.5_0_tal.xfm What’s wrong? Would you tell me how to resolve? Thank you in advance! Feng-Xian

Re: [Freesurfer] mri_convert

of lh.thickness.asc is different from the shows of terminal. Have something wrong of these commands? Thank you in advance! Feng-Xian On Mon, 19 Jan 2009 10:01:21 -0500 (EST), Bruce Fischl wrote read the mris_convert help. You can convert the surfaces to ascii as well (e.g. mris_convert lh.white

Re: [Freesurfer] image matrix

of surface which I want to get. Right? If not, which value is I want to get? Then, I run lh.orig and another subjects, I find the value is different from those. So, the vertices number of surface is not a fixed value and changes with hemispheres and subjects. Thank you in advance!! Feng-Xian On Wed, 8

Re: [Freesurfer] contrast matrix

or to consult? Thank you in advance!! Feng-Xian On Wed, 08 Jul 2009 15:28:44 -0400, Douglas N Greve wrote You can't do that with a contrast matrix. In general, you can't test ANDs with a contrast, you have to test ORs. For AND, you have to use a conjunction in which you make two contrasts

Re: [Freesurfer] make_average_subject error about limit

lh.noise_0.5- 1.glmdir The terminal shows: ERROR: Option --cortex unknown Would you tell me what’s wrong? And how do I do to solve this error? Thank you in advance! Feng-Xian On Tue, 07 Jul 2009 11:49:32 -0400, Douglas N Greve wrote Is there a space between -- and hemi? caching is just a way

[Freesurfer] contrast matrix

Hi, I want to analysis three independence groups. And, I want to display a result of A group B group C group with positive(red) and A group B group C group with negative(blue). To show that, how do I write the number of columns in the contrast matrix? Thank you in advance! Feng-Xian

Re: [Freesurfer] make_average_subject error about limit

job to analysis, and, I want to change the analysis method from QDEC to DODS) So, which way do I choose to analysis my subjects?? Idon't understand the differences from them. Thank you in advance! Feng-Xian On Fri, 26 Jun 2009 15:25:12 -0400, Nick Schmansky wrote in general

[Freesurfer] image matrix

for each subject. If yes, what text has the information of the value of cortical thickness and where do I find that text? If no, how can I get the information? Thank you in advance! Feng-Xian - Chang Gung University Mail Server Web Mail system By Chang

[Freesurfer] make_average_subject error about limit

. But, I encounter the problem about make_average_subject. When I type: make_average_subject --subects subjid1 subjid2 ... the terminal show that: limit: descriptors: Can't remove limit What's wrong about the command I type? And, how to solve the problem? Thank you in advance! Feng-Xian

[Freesurfer] group analysis with one factor and three levels

to do? If not, would you suggest me any other way to get the group analysis? Thank you in advance! Feng-Xian - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic

[Freesurfer] cortical thickness value of each pixel

. Could you suggest me how to calculate the global thickness statistics or tell me where to get the file regarding cortical thickness values of each pixel? Thank you in advance! Feng-Xian - Chang Gung University Mail Server Web Mail system

[Freesurfer] segmentation

of these two groups (1% vs 5%) has a bias. Would you get me some comment? I guess the finding of bias maybe has a great relationship with the process of segmentation. Would you tell me what to do segmentation in FreeSuefer? Thank you in advance! Feng-Xian

[Freesurfer] cortical thickness maps

to Windows XP? Thanks in advance! Feng-Xian - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list

[Freesurfer] cortical thickness maps

to Windows XP? Thanks in advance! Feng-Xian - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list

[Freesurfer] mri_convert

). What can I do to convert these formats to analysis format or nifti? Thanks in advance! Feng-Xian - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic

[Freesurfer] open *.mgh

Hi, Thank you for your help before. And, I have a problem today. How do I open the file called *.mgh as F.mgh and sig.mgh in the dictionary “qedc”? This problem has been nagging me for some time. Thank you in advance! Feng-Xian - Chang Gung

[Freesurfer] Talairach coordinates

coordinates.* 1) Does the surface coordinates differ from Talairach coordinates? 2) If yes, can I translate the surface coordinates to Talairach coordinates? And how do I do? Does Freesurfer have some methods to do that? Thank you in advance. Feng-Xian

[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.

[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

[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

[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

[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.

Re: [Freesurfer] problems

11:49:43 CST 2007 Thank you 2007/10/9, Nick Schmansky [EMAIL PROTECTED]: Feng-Xian, If you have fedora core 4, then you should the centos4 build of freesurfer which is built against the libstdc++.so.6 libs, unlike the rh9 build of freesurfer, which it appears you are using, which

[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

[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

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.