[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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] map .xls or .txt file to fsaverage
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 > 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 > fis...@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 ><mailto:fis...@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 ><mailto: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 >> >>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 >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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 > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] map .xls or .txt file to fsaverage
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 > 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 >> >> 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 >>>> >>>> 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] map .xls or .txt file to fsaverage
Hi, They have the same coordinates. Before I run MATLAB to obtain the analysis of anova, I mapped the cortical thickness value of each subject to fsaverage using mri_surf2surf and then I obtained the asc file with the coordinates of 65536 vertices and their thickness value. Now, I want to map the results of anova to fsaverage. Could these results do that? Or, you could recommend me another way to obtain the same map. Thank you in advance! Feng-Xian 2009/10/1 Douglas N Greve > If you are combining data across subjects in your matlab program, aren't > they already 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, >>> >>> 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 >>> >>> >>> >>>> 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 >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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 > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 > 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 >> >> 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] map .xls or .txt file to fsaverage
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 > 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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/mailman/listinfo/freesurfer
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 step, I use mris_convert to show the cortical thickness value of this > subject on this MNI coordinates. But, this has an error as follows. > mris_convert -c subject/surf/lh.thickness fsaverage /surf/lh.white > lh.subject.thickness.asc > > > ERROR: number of vertices in subject/surf/lh.thickness does not match > surface (154962,163842) > > I know what’s happen, but I don’t know how to solve. > > I want to obtain the asc file containing the same vertices as fsaverage and > with the cortical thickness value and their coordinates in the file. Could > you teach me how to obtain the match fsaverage surface file? > > Thank you in advance! > > Feng-Xian > > > > > > > 2009/8/20 Bruce Fischl > > you can use mri_surf2surf to map them all the fsaverage, then mris_convert >> to convert each one to asciii. >> >> cheers >> Bruce >> >> On Thu, 20 Aug 2009, Feng-Xian Yan wrote: >> >> 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 >>> >>> >>>> Yes, this is what our group analysis 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 another problem want to solve. I check the number of vertex for >>>>> all >>>>> subjects, but I found that the number of vertex for each subjects and >>>>> each >>>>> hemispheres is different. Because I want to compare cortical thickness >>>>> using >>>>> vertex-by-vertex, I 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 >>>>> >>>>> >>>>> >>>>> >>>>> 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 file are in MNI305 space. You can see this in >>>>>> >>>>>>> tksurfer with View->Configure->Information and select the mni305 >>>>>>> button. >>>>>>> >>>>>>> Feng-Xian Yan wrote: >>>>>>> >>>>>>> >>>>>>> Thank you for your response. >>>>>>>> >>>>>>>> So, you mean that I have to do "mris_convert" two times. One for >>>>>>>> lh.white.tal.asc, another for lh.thickness.asc. And the Tal >>>>>>>> coordinates >>>>>>>> in >>>>>>>> lh.white.tal.asc file corresponds to the cortical thickness value in >>>>>>>> lh.th
[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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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 > > Yes, this is what our group analysis 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 another problem want to solve. I check the number of vertex for >> all >> subjects, but I found that the number of vertex for each subjects and each >> hemispheres is different. Because I want to compare cortical thickness >> using >> vertex-by-vertex, I 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 >> >> >> >> >> 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 file are in MNI305 space. You can see this in >>>> tksurfer with View->Configure->Information and select the mni305 button. >>>> >>>> Feng-Xian Yan wrote: >>>> >>>> >>>>> Thank you for your response. >>>>> >>>>> So, you mean that I have to do "mris_convert" two times. One for >>>>> lh.white.tal.asc, another for lh.thickness.asc. And the Tal coordinates >>>>> in >>>>> lh.white.tal.asc file corresponds to the cortical thickness value in >>>>> lh.thickness.asc file. >>>>> >>>>> >>>>> But, the Tal coordinates in lh.white.tal.asc is difference from the >>>>> result in the tksurfer tool box. That is to say, when I open this >>>>> subject by >>>>> tksurfer, I look at the coordinate of the vertex Tal in the tksurfer >>>>> tool >>>>> box, and the coordinate is difference from the coordinates that obtain >>>>> from >>>>> the command ?mris_convert ?c lh.thickness lh.white lh.thickness.asc?. >>>>> >>>>> >>>>> What do have some problems? >>>>> >>>>> >>>>> Thank you in advance! >>>>> >>>>> >>>>> Feng-Xian >>>>> >>>>> >>>>> 2009/8/18 Douglas N Greve >>>> gr...@nmr.mgh.harvard.edu>> >>>>> >>>>> You have convert the thickness file (lh.thickness) to ascii like >>>>> you did >>>>> with the surface (with mris_convert). You will then have two >>>>> files, and >>>>> the second file will have the thickness values. >>>>> >>>>> doug >>>>> >>>>> Feng-Xian Yan wrote: >>>>> > >>>>> > Hi, >>>>> > >>>>> > Sorry, I don't know what you mean. I know each lines is a vertex and >>>>> > represent a Tal coordinate, but each lines only contain xyz, but not >>>>> > contain cortical thickness value of these coordinates. That is >>>>> to say, >>>>> > the following is >>>>> > >>>>> > Tal x Tal y Tal z >>>>> > >>>>> > -13.424789 -125.068245 12.671550 0 >>>>> > >>>>> > What?s wrong do I think? >>>>> > >>>>> > Thank you in advance. >>>>> > >>>>> > Feng-Xian >>>>> > >>>>> > 2009/8/18 Douglas N Greve >>>> <mailto:gr...@nmr.mgh.harvard.edu> >>>>> > <mailto:gr...@nmr.mgh.harvard.edu >>>>> <mailto:gr...@nmr.mgh.harvard.edu>>> >>>>> > >>>>
Re: [Freesurfer] thickness map
Hi, Thank you for your responses before. I have another problem want to solve. I check the number of vertex for all subjects, but I found that the number of vertex for each subjects and each hemispheres is different. Because I want to compare cortical thickness using vertex-by-vertex, I 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 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 file are in MNI305 space. You can see this in >> tksurfer with View->Configure->Information and select the mni305 button. >> >> Feng-Xian Yan wrote: >> >>> >>> Thank you for your response. >>> >>> So, you mean that I have to do "mris_convert" two times. One for >>> lh.white.tal.asc, another for lh.thickness.asc. And the Tal coordinates in >>> lh.white.tal.asc file corresponds to the cortical thickness value in >>> lh.thickness.asc file. >>> >>> >>> But, the Tal coordinates in lh.white.tal.asc is difference from the >>> result in the tksurfer tool box. That is to say, when I open this subject by >>> tksurfer, I look at the coordinate of the vertex Tal in the tksurfer tool >>> box, and the coordinate is difference from the coordinates that obtain from >>> the command “mris_convert –c lh.thickness lh.white lh.thickness.asc”. >>> >>> >>> What do have some problems? >>> >>> >>> Thank you in advance! >>> >>> >>> Feng-Xian >>> >>> >>> 2009/8/18 Douglas N Greve >> gr...@nmr.mgh.harvard.edu>> >>> >>>You have convert the thickness file (lh.thickness) to ascii like >>>you did >>>with the surface (with mris_convert). You will then have two >>>files, and >>>the second file will have the thickness values. >>> >>>doug >>> >>>Feng-Xian Yan wrote: >>>> >>>> Hi, >>> > >>>> Sorry, I don't know what you mean. I know each lines is a vertex and >>>> represent a Tal coordinate, but each lines only contain xyz, but not >>>> contain cortical thickness value of these coordinates. That is >>>to say, >>>> the following is >>>> >>>> Tal x Tal y Tal z >>>> >>>> -13.424789 -125.068245 12.671550 0 >>>> >>>> What’s wrong do I think? >>>> >>>> Thank you in advance. >>>> >>>> Feng-Xian >>>> >>>> 2009/8/18 Douglas N Greve >><mailto:gr...@nmr.mgh.harvard.edu> >>> > <mailto:gr...@nmr.mgh.harvard.edu >>><mailto:gr...@nmr.mgh.harvard.edu>>> >>>> >>>> Just convert the lh.thickness to ascii as well. Each line of the >>>> xyz coords corresponds to a line in the thickness ascii >>>(each line >>>> is a vertex). >>>> >>>> >>>> doug >>>> >>>> Feng-Xian Yan wrote: >>>> >>>> >>>> Hi, >>>> >>>> I try it again with you recommend me, but the produced asc >>>> file (lh.white.tal.asc) only contain x, y, z >>>coordinates. (The >>>> following shows that.) >>>> >>>> >>>> #!ascii version of lh.white.tal >>>> >>>> 155006 310008 >>>> >>>> -13.424789 -125.068245 12.671550 0 >>>> >>>> -13.939213 -125.063232 12.714314 0 >>>> >>>> -14.861158 -125.268639 12.404987 0 >>>> >>>> >>>> >>>> But, I want to have cortical thickness value with Tal >>>> coordinates. This file doesn’t satisfy our demand. >>>> >>>> >>>> Our dema
[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 voxels containing A group > B group > C group and A group < B group < C group, Freesurfer can’t do that. So, we want to get this map by myself and use Matlab or other tool to obtain that. And, now I want to obtain a file that containing the Tal coordinate and the thickness value of this coordinate for all subjects. Would you tell me how to get the file that containing the Tal coordinate and the thickness value of this coordinate? (2) Before, I want to use the following command to get the thickness value. The command line is "mri_surf2surf --srcsubject noise0.5_0 --srcsurfval thickness --sfmt surface --trgsubject noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --tfmt surface --hemi lh --sval-tal-xyz orig --tval-xyz", and then i type “mris_convert lh.noise0.5_0_tal.xfm lh.white lh.thickness.asc”. But, the result file(lh.thickness.asc) does not contain the thickness value of this coordinate. So, I think these commands have some error. (3) Use the command “mris_convert –c lh.thickness lh.white lh.thickness.asc” to obtain the thickness value of the RAS coordinates. But, I’m confused about that if I change lh.white to lh.pail or lh.inflated. What’s difference for the three? (4) And, I ask some problem before. Everyone said the result file(lh.thickness.asc) is using RAS coordinates through “mris_convert –c lh.thickness lh.white lh.thickness.asc”. But, I have confused about this. When I open this subject by tksurfer, I look at the coordinate of the vertex RAS in the tksurfer tool box, and the coordinate is difference from the coordinates that obtain from the command “mris_convert –c lh.thickness lh.white lh.thickness.asc”. So, which one is right? Thank you in advance! Feng-Xian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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: > > > > Hi, > > > > I try again with you said. First, I type this command“mri_surf2surf > > --srcsubject noise0.5_0 --srcsurfval thickness --sfmt curv > > --trgsubject noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --tfmt curv > > --hemi lh --sval-tal-xyz orig --tval-xyz”, then I type “mris_convert > > -c lh.noise0.5_0_tal.xfm lh.white lh.thickness.asc”. > > > > But, the error is the same.” MRISreadBinaryCurvature: incompatible > > vertex number in file ./lh.noise0.5_0_tal.xfm” > > > > > > What’s wrong? Would you help me to resolve this problem? Because I > > really want to obtain the thickness ascii file with Tal coordinate. > > Or, have you another method to obtain the thickness ascii file with > > Tal coordinate? > > > > Thank you in advance! > > > > Feng-Xian > > > > > > > > 2009/8/4 Bruce Fischl > <mailto:fis...@nmr.mgh.harvard.edu>> > > > > you need to tell it what format to write the output in. Try using - > > --tfmt curv > > > > I would have thought you needed --sfmt curv also. I'm just > > 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.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 ?the > > coordinates > > are native RAS. You can use mri_surf2surf to convert the > > surface to tal > > coords with the talairach.xfm.? > > > > > > > > So, first, I change the native RAS cooridinate to Tal > > coordinate with > > ?mri_surf2surf --srcsubject noise0.5_0 --srcsurfval thickness > > --trgsubject > > noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --hemi lh > > --sval-tal-xyz orig > > --tval-xyz? > > > > srcsubject = noise0.5_0 > > srcval = thickness > > srctype = > > trgsubject = noise0.5_0 > > trgval = noise0.5_0_tal.xfm > > trgtype = > > surfreg = sphere.reg > > srchemi = lh > > trghemi = lh > > frame = 0 > > fwhm-in = 0 > > fwhm-out = 0 > > Reading source surface reg > > > /usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.sphere.reg > > Loading source data > > Reading surface file > > > /usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.orig > > Applying MNI305 talairach transform > > 0.966 0.002 -0.004 0.426; > > 0.018 0.989 0.041 -19.382; > > -0.006 0.032 0.962 17.438; > > 0.000 0.000 0.000 1.000; > > INFO: surfcluster: NOT fixing group surface area > > INFO: trgsubject = srcsubject > > Saving target data > > > > > > > > Then, I obtain the thickness asc file with Tal coordinate > > using this command > > ?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 > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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 > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ascii file
Hi, I try again with you said. First, I type this command“mri_surf2surf --srcsubject noise0.5_0 --srcsurfval thickness --sfmt curv --trgsubject noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --tfmt curv --hemi lh --sval-tal-xyz orig --tval-xyz”, then I type “mris_convert -c lh.noise0.5_0_tal.xfm lh.white lh.thickness.asc”. But, the error is the same.” MRISreadBinaryCurvature: incompatible vertex number in file ./lh.noise0.5_0_tal.xfm” What’s wrong? Would you help me to resolve this problem? Because I really want to obtain the thickness ascii file with Tal coordinate. Or, have you another method to obtain the thickness ascii file with Tal coordinate? Thank you in advance! Feng-Xian 2009/8/4 Bruce Fischl > you need to tell it what format to write the output in. Try using - > --tfmt curv > > I would have thought you needed --sfmt curv also. I'm just 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.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 ?the coordinates >> are native RAS. You can use mri_surf2surf to convert the surface to tal >> coords with the talairach.xfm.? >> >> >> >> So, first, I change the native RAS cooridinate to Tal coordinate with >> ?mri_surf2surf --srcsubject noise0.5_0 --srcsurfval thickness --trgsubject >> noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --hemi lh --sval-tal-xyz orig >> --tval-xyz? >> >> srcsubject = noise0.5_0 >> srcval = thickness >> srctype= >> trgsubject = noise0.5_0 >> trgval = noise0.5_0_tal.xfm >> trgtype= >> surfreg= sphere.reg >> srchemi= lh >> trghemi= lh >> frame = 0 >> fwhm-in= 0 >> fwhm-out = 0 >> Reading source surface reg >> >> /usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.sphere.reg >> Loading source data >> Reading surface file >> >> /usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.orig >> Applying MNI305 talairach transform >> 0.966 0.002 -0.004 0.426; >> 0.018 0.989 0.041 -19.382; >> -0.006 0.032 0.962 17.438; >> 0.000 0.000 0.000 1.000; >> INFO: surfcluster: NOT fixing group surface area >> INFO: trgsubject = srcsubject >> Saving target data >> >> >> >> Then, I obtain the thickness asc file with Tal coordinate using this >> command >> ?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 >> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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 “the coordinates are native RAS. You can use mri_surf2surf to convert the surface to tal coords with the talairach.xfm.” So, first, I change the native RAS cooridinate to Tal coordinate with “mri_surf2surf --srcsubject noise0.5_0 --srcsurfval thickness --trgsubject noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --hemi lh --sval-tal-xyz orig --tval-xyz” srcsubject = noise0.5_0 srcval = thickness srctype= trgsubject = noise0.5_0 trgval = noise0.5_0_tal.xfm trgtype= surfreg= sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 0 Reading source surface reg /usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.sphere.reg Loading source data Reading surface file /usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.orig Applying MNI305 talairach transform 0.966 0.002 -0.004 0.426; 0.018 0.989 0.041 -19.382; -0.006 0.032 0.962 17.438; 0.000 0.000 0.000 1.000; INFO: surfcluster: NOT fixing group surface area INFO: trgsubject = srcsubject Saving target data Then, I obtain the thickness asc file with Tal coordinate using this command “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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ascii file
Hi, I have two problems want to solve. First, I want to know what coordinates it is, when I type the following command. mris_convert -c lh.thickness lh.white lh.thickness.asc Is it Tal coordinate?? Second, if the asc file doesn't use Tal coordinate, what commands do I type to obtain ? Bcause I really want to get the thickness asc with Tal coordinate. 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert
Hi, Thank you for your response. I want to make sure the command as follows. If I want to obtain the thickness ascii with Tal coordinate, can the following commands make I to obtain? First, I change the coordinate from Freesurfer to Tal using the command. mris_convert –t subjid lh.pial lh.pial.tal Then, I obtain the thickness ascii with Tal coordinate from the following command. mris_convert -c lh.thickness lh.pial.tal lh.thickness.asc Finally, I want to check whether the coordinate is true or not. So I open tksurfer to check. But, I found the vertex Tal coordinate 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 lh.white.asc) > > cheers > Bruce > On Mon, 19 Jan 2009, Feng-Xian > wrote: > > > > > Hi Bruce > >Thanks for your answer. But I really want to get the result of surfaces > > on FreeSurfer and I would like to read these surfaces (e.g. lh inflated, lh > > thickness) on Windows XP. > > > > Would you teach me how can I get these? > > > > Thanks in advance! > > Feng-Xian > > > > > > > > On Mon, 19 Jan 2009 09:05:59 -0500 (EST), Bruce Fischl wrote > >> Hi Feng-Xian, > >> > >> mri_convert only works on volumes, and to convert e.g. the orig.mgz > >> volume to nifti use: > >> > >> mri_convert orig.mgz orig.nii > >> > >> cheers, > >> Bruce > >> > >> On Mon, 19 > >> Jan 2009, Feng-Xian wrote: > >> > >>> > >>> Hi, > >>> I am finished to run my subjects using recon-all and I would like to > > know > >>> the usage of mri_convert to convert the results of FreeSurfer into the > >>> analyze format or nifti. > >>> > >>> Some of the results of FreeSurfer are volumes (e.g. brainmask.mgz) and > > some > >>> of them are surfaces (e.g. lh inflated). > >>> > >>> 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 mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> > > > > > > - > > Chang Gung University Mail Server Web Mail system > > By Chang-Gung University Information Center > > (http://www.cgu.edu.tw/ic/) > > > > > > - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] image matrix
Hi,
Thank you for your response! I use the command what you said.
The terminal shows:
euler # = v-e+f = 2g-2: 154901 - 464697 + 309798 = 2 --> 0 holes
F =2V-4: 309798 = 309802-4 (0)
2E=3F:929394 = 929394 (0)
I guess that 929394 is the vertices number 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 Jul 2009 17:19:20 -0400 (EDT), Bruce Fischl wrote
> what is noise0.5_0? It isn't a surface file given the output of
> mris_euler_number. Try running
>
> mris_euler_number rh.orig
>
> On Thu, 9 Jul 2009, Feng-Xian wrote:
>
> > Hi,
> > Thank you for your response! But, I canÿÿt find vertices number of a
> > surface through typing the following command:
> > mris_euler_number noise0.5_0
> >
> > When I type the command, the terminal shows some information as follow.
> >
> > euler # = v-e+f = 2g-2: 0 - 0 + 0 = 0 --> 1 holes
> > F =2V-4: 0 != 0-4 (-4)
> > 2E=3F:0 = 0 (0)
> > total defect index = 2
> >
> > But I donÿÿt know what meaning of the numbers is. Would you tell me?
> > And, have any other ways to get the vertices number of a surface?
> >
> > Then, I want to make sure that is image matrix 256 x 256 x 256?
> >
> > Thank you for in advance!!
> >
> > Feng-Xian
> >
> >
> > On Tue, 30 Jun 2009 07:39:31 -0400 (EDT), Bruce Fischl wrote
> >> Hi Feng-Xian,
> >>
> >> the surfaces all live in the surf subdirectory. To see how many
> >> vertices a surface contains you can run either mris_euler_numer of
> >> mris_info. The thickness is in the ?h.thickness ("curv" format file -
> >> one scalar per vertex) and the inflated is in ?h.inflated surface
> >> format. You can visualize the thickness in tksurfer by loading the
> >> inflated surface then loading the thickness from the file menu using
> >> the load curvature option.
> >>
> >> cheers
> >> Bruce
> >>
> >> On Tue, 30 Jun 2009, Feng-Xian wrote:
> >>
> >>>
> >>> Hi,
> >>> I want to check the image matrix after doing autorecon-all. When I
look
> >>> at the text, I see that ÿÿOriginal Data has (1, 1, 1) mm size and (224,
> > 256,
> >>> 160) voxels. Data is conformed to 1 mm size and 256 voxels for all
> >>> directionsÿÿ. This is said that that image matrix is 256 x 256 x 256.
> > Right?
> >>>
> >>> And, I want to know how many voxels do an inflated surface have?
Where
> >>> dir and what text do I to get that?
> >>>
> >>> And, do FreeSurfer have a text that including the value of cortical
> >>> thickness? I want to know the information of cortical thicknessÿÿs
value
> > at
> >>> all pixels of whole brain 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-Gung University Information Center
> >>> (http://www.cgu.edu.tw/ic/)
> >>>
> >>> ___
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>
> >>>
> >>>
> >
> >
> > -
> > Chang Gung University Mail Server Web Mail system
> > By Chang-Gung University Information Center
> > (http://www.cgu.edu.tw/ic/)
> >
> >
> >
-
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___
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Re: [Freesurfer] contrast matrix
Hi, I think that I know what you mean. So, if I want to get the result with A > B > C, I should get A > B and B > C, respectively. And then, to combine these two results. Would you tell me detail with step by step and what command I should type and how to type ? Or, have some reference to follow 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 A > B and B > C, > threshold both (mri_binarize), then do a logical AND. > > doug > > Feng-Xian wrote: > > 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 > > > > > > > > - > > Chang Gung University Mail Server Web Mail system > > By Chang-Gung University Information Center > > (http://www.cgu.edu.tw/ic/) > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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 - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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 - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] image matrix
Hi,
Thank you for your response! But, I can’t find vertices number of a
surface through typing the following command:
mris_euler_number noise0.5_0
When I type the command, the terminal shows some information as follow.
euler # = v-e+f = 2g-2: 0 - 0 + 0 = 0 --> 1 holes
F =2V-4: 0 != 0-4 (-4)
2E=3F:0 = 0 (0)
total defect index = 2
But I don’t know what meaning of the numbers is. Would you tell me?
And, have any other ways to get the vertices number of a surface?
Then, I want to make sure that is image matrix 256 x 256 x 256?
Thank you for in advance!!
Feng-Xian
On Tue, 30 Jun 2009 07:39:31 -0400 (EDT), Bruce Fischl wrote
> Hi Feng-Xian,
>
> the surfaces all live in the surf subdirectory. To see how many
> vertices a surface contains you can run either mris_euler_numer of
> mris_info. The thickness is in the ?h.thickness ("curv" format file -
> one scalar per vertex) and the inflated is in ?h.inflated surface
> format. You can visualize the thickness in tksurfer by loading the
> inflated surface then loading the thickness from the file menu using
> the load curvature option.
>
> cheers
> Bruce
>
> On Tue, 30 Jun 2009, Feng-Xian wrote:
>
> >
> > Hi,
> > I want to check the image matrix after doing autorecon-all. When I look
> > at the text, I see that ÿÿOriginal Data has (1, 1, 1) mm size and (224,
256,
> > 160) voxels. Data is conformed to 1 mm size and 256 voxels for all
> > directionsÿÿ. This is said that that image matrix is 256 x 256 x 256.
Right?
> >
> > And, I want to know how many voxels do an inflated surface have? Where
> > dir and what text do I to get that?
> >
> > And, do FreeSurfer have a text that including the value of cortical
> > thickness? I want to know the information of cortical thicknessÿÿs value
at
> > all pixels of whole brain 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-Gung University Information Center
> > (http://www.cgu.edu.tw/ic/)
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
-
Chang Gung University Mail Server Web Mail system
By Chang-Gung University Information Center
(http://www.cgu.edu.tw/ic/)
___
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Re: [Freesurfer] make_average_subject error about limit
Hi, Thank you for your response! I solve this problem of mris_preproc. The next step is to do mri_glmfit. And, when I type the following command: mri_glmfit --y lh.noise_0.5-1-5.thickness.10.mgh --fsgd noise_0.5-1-5.fsgd dods --C noise_0.5-1.mtx --surf fsaverage lh --cortex --glmdir 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 to speed some analyses by pre-smoothing and > sampling to the standard space. > > doug > > Feng-Xian wrote: > > Hi, > > > >I copied the default average subject from $FREESURFER_HOME/subjects dir > > to my analysis dir. > > > > Then, I make a FSGD file and some contrast matrices and put them into my > > analysis dir. > > > > After that, I start to run group analysis. > > > > But, when I type the following commands: > > > > mris_preproc --fsgd noise_0.5-1-5.fsgd --target fsaverage -- hemi lh -- meas > > thickness --out lh.noise_0.5-1-5.thickness.00.mgh > > > > The terminal shows: > > > > ERROR: flag -- not recognized > > > > > > Now, I have two problems want to ask. > > > > 1) What's wrong about the commands that I type? And, how to solve the > >problem? > > > > 2) I found this commands from the FreeSurfer web. And, I'm confused about > >that two ways to do analysis. > > One is cached (qcached) data, and the other is uncached data. What's > >way is suitable to my subjects? (My subjects is one factor and three > >levels, had run QDEC before, but QDEC is not good 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, it is not necessary to run make_average_subject prior to > >> performing an analysis. using the default average subject that > >> freesurfer provides, named 'fsaverage', is sufficient for most cases, > >> because it doesnt affect the analysis, its only used as a target upon > >> which to project results. the 'fsaverage' subject is in the > >> $FREESURFER_HOME/subjects dir, and you should copy it to your own > >> SUBJECTS_DIR prior to performing any group analysis. > >> > >> Nick > >> > >> On Fri, 2009-06-26 at 10:48 +0800, Feng-Xian wrote: > >> > >>> Hi, > >>> > >>>I know I wont to do QDEC now, so I want to change the method of group > >>> analysis from QDEC to the web you tell me. But, I did QDEC before. > >>> > >>> Before I do DODS, should I do make_average_subject to view the result of > >>> > > my > > > >>> subjects? Or, I have another method to view the results?? > >>> > >>> Thank you in advance! > >>> > >>> Feng-Xian > >>> > >>> > >>> > >>> > >>> On Thu, 25 Jun 2009 12:01:21 -0400, Nick Schmansky wrote > >>> > >>>> Feng-xian, > >>>> > >>>> I should also mention that i dont think creating your own average > >>>> subject will solve the problem you describe, where you need to work > >>>> > > with > > > >>>> three levels in your group. for that, you wont be able to use qdec, > >>>> but will need to run things manually. these pages give examples: > >>>> > >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples > >>>> > >>>> and note one of them is 1 Factor, 3 Levels. > >>>> > >>>> Nick > >>>> > >>>> On Thu, 2009-06-25 at 11:55 -0400, Nick Schmansky wrote: > >>>> > >>>>> Feng-Xian, > >>>>> > >>>>> It appears that you do not have permission on your system to change > >>>>> > > the > > > >>>>> limits. So you will have to edit the scripts make_average_volume, > &g
Re: [Freesurfer] make_average_subject error about limit
Hi, I copied the default average subject from $FREESURFER_HOME/subjects dir to my analysis dir. Then, I make a FSGD file and some contrast matrices and put them into my analysis dir. After that, I start to run group analysis. But, when I type the following commands: mris_preproc --fsgd noise_0.5-1-5.fsgd --target fsaverage -- hemi lh --meas thickness --out lh.noise_0.5-1-5.thickness.00.mgh The terminal shows: ERROR: flag -- not recognized Now, I have two problems want to ask. 1) What's wrong about the commands that I type? And, how to solve the problem? 2) I found this commands from the FreeSurfer web. And, I'm confused about that two ways to do analysis. One is cached (qcached) data, and the other is uncached data. What's way is suitable to my subjects? (My subjects is one factor and three levels, had run QDEC before, but QDEC is not good 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, it is not necessary to run make_average_subject prior to > performing an analysis. using the default average subject that > freesurfer provides, named 'fsaverage', is sufficient for most cases, > because it doesnt affect the analysis, its only used as a target upon > which to project results. the 'fsaverage' subject is in the > $FREESURFER_HOME/subjects dir, and you should copy it to your own > SUBJECTS_DIR prior to performing any group analysis. > > Nick > > On Fri, 2009-06-26 at 10:48 +0800, Feng-Xian wrote: > > Hi, > > > >I know I wont to do QDEC now, so I want to change the method of group > > analysis from QDEC to the web you tell me. But, I did QDEC before. > > > > Before I do DODS, should I do make_average_subject to view the result of my > > subjects? Or, I have another method to view the results?? > > > > Thank you in advance! > > > > Feng-Xian > > > > > > > > > > On Thu, 25 Jun 2009 12:01:21 -0400, Nick Schmansky wrote > > > Feng-xian, > > > > > > I should also mention that i dont think creating your own average > > > subject will solve the problem you describe, where you need to work with > > > three levels in your group. for that, you wont be able to use qdec, > > > but will need to run things manually. these pages give examples: > > > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples > > > > > > and note one of them is 1 Factor, 3 Levels. > > > > > > Nick > > > > > > On Thu, 2009-06-25 at 11:55 -0400, Nick Schmansky wrote: > > > > Feng-Xian, > > > > > > > > It appears that you do not have permission on your system to change the > > > > limits. So you will have to edit the scripts make_average_volume, > > > > make_average_surface and make_average_subject to comment out the 'limit' > > > > line, so that it looks like this: > > > > > > > > #limit descriptors unlimited > > > > > > > > > > > > Nick > > > > > > > > On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote: > > > > > Hi, > > > > > > > > > >I have a problem with make_average_subject. > > > > > > > > > > After running all commands (including ln -s > > > > > $FREESURFER_HOME/subjects/fsaverage > > > > > and recon-all -s -qcache for all my subjects) about running > > QDEC, I > > > > > found that QDEC could not analysis my group. > > > > > > > > > > Because the group have 1 factor and three levels, QDEC can't run. > > > > > > > > > > So, I want to change the method of analysis from QDEC to DODS. > > > > > > > > > > > > > > > I had a fsaverage file when I running QDEC, but the fsaverage did not > > use my > > > > > subjects to make. > > > > > > > > > > So, can I use the fsaverage file to run DODS? > > > > > > > > > > If not, I should make a new fsaverage with my subjects. > > > > > > > > > > But, I encounter the problem about make_average_subject. > > > > > > > > > > > > > > > When I type: > > > > > > > > > > make_average_subje
[Freesurfer] image matrix
Hi, I want to check the image matrix after doing autorecon-all. When I look at the text, I see that “Original Data has (1, 1, 1) mm size and (224, 256, 160) voxels. Data is conformed to 1 mm size and 256 voxels for all directions”. This is said that that image matrix is 256 x 256 x 256. Right? And, I want to know how many voxels do an inflated surface have? Where dir and what text do I to get that? And, do FreeSurfer have a text that including the value of cortical thickness? I want to know the information of cortical thickness’s value at all pixels of whole brain 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-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] make_average_subject error about limit
Hi, I have a problem with make_average_subject. After running all commands (including ln -s $FREESURFER_HOME/subjects/fsaverage and recon-all -s -qcache for all my subjects) about running QDEC, I found that QDEC could not analysis my group. Because the group have 1 factor and three levels, QDEC can't run. So, I want to change the method of analysis from QDEC to DODS. I had a fsaverage file when I running QDEC, but the fsaverage did not use my subjects to make. So, can I use the fsaverage file to run DODS? If not, I should make a new fsaverage with my subjects. But, I encounter the problem about make_average_subject. When I type: make_average_subject --subects ... 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 - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] make_average_subject error about limit
Hi, I have a problem with make_average_subject. After running all commands about running QDEC, I found that QDEC could not analysis my group. Because the group I want to analysis have 1 factor and three levels, QDEC can't run. So, I want to change the method of analysis from QDEC to FSGD. But, I have a problem about FSGD. When I type: make_average_subject --subects ... the terminal show that: limit: descriptors: Can't remove limit (此項操作並不被允許) What's wrong about the command I type? And, how to solve the problem? 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] group analysis with one factor and three levels
Hi, I have a problem of group analysis with QDEC. Now, I want to analysis a group with one factor and three levels. When I run QDEC with this group, the terminal shows error with too many levels. So, how can I do to analysis this group with one factor and three levels? Would you tell me what 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] cortical thickness value of each pixel
Hi, I want to calculate the global thickness statistics (mean +/- SD) for all my subjects. And, I could calculate the global thickness statistics by some information about cortical thickness values of each pixel. But I can’t find any files regarding cortical thickness values 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 By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] segmentation
Hi, I have some problem. Could you get me some suggestion? I get a simulation brain with no-adding noise from BrainWeb. Then, I add 1% noise and 5% noise, respectively, to the simulation brains. When I finished these simulation brains through FreeSurfer, I found that the cortical thickness 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 - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] cortical thickness maps
Hi, Thank you for your help before. I finished the group analysis of cortical thickness with QDEC on FreeSurfer and I would like to get the cortical thickness maps with inflated surface on Windows XP. Would you teach me how can I change the cortical thickness maps from FreeSurfer 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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] cortical thickness maps
Hi, Thank you for your help before. I finished the group analysis of cortical thickness with QDEC on FreeSurfer and I would like to get the cortical thickness maps with inflated surface on Windows XP. Would you teach me how can I change the cortical thickness maps from FreeSurfer 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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert
Hi, I am finished to run my subjects using recon-all and I would like to know the usage of mri_convert to convert the results of FreeSurfer into the analyze format or nifti. Some of the results of FreeSurfer are volumes (e.g. brainmask.mgz) and some of them are surfaces (e.g. lh inflated). 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] thickness value
Hi, I gain the cortical thickness value and other information of all ROIs for all my subjects (found in $FREESURFER_HOME/subjects/filename/stats). But, can I gain the cortical thickness value and other information of all vertices for all my subjects? I want to gain the values, not maps. 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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 University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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. What model is the surface coordinates used? Second, after analyzing the thickness, it shows the color bar's scale in p-value. How do I do to change the scale from p-value to mm? . ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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 $SUBJECTS_DIR/group_analysis cd $SUBJECTS_DIR Then, I run the pre-smoothed fsaverage surfaces recon-all -s subjects1 -qcache Could you tell me what's wrong? Thank you~~ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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 physical sizes are (1404.00 mm, 256.00 mm, 256.00 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 1404 slices. The freesurfer tools should be able to handle more than 256 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). ==== This problem confused me. What can I do? Could you tell me what image is freesurfer I can run and get the best results? (about dimension…. ) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 [EMAIL PROTECTED]:/usr/local/freesurfer/subjects/x249/mri/] [2007-12-13 11:49:43] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_4619/ ./tmp.mri_nu_correct.mni.4568/nu0.mnc ./tmp.mri_nu_correct.mni.4568/nu1.imp /usr/local/freesurfer/mni/bin/volume_stats: error while loading shared libraries: libstdc++.so.5: cannot open shared object file: No such file or directory nu_estimate_np_and_em: crashed while running volume_stats (termination status=32512) nu_correct: crashed while running nu_estimate_np_and_em (termination status=32512) ERROR: nu_correct Linux localhost.localdomain 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Thu Dec 13 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 is built against the > libstdc++.so.5 libs. > > Nick > > > > 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_convert x249.img 001.mgz > >> 2) It's missing libstd++.so.5. I suggest you run find / -name "libstd*" > >> -print > >> If you find a libstd++.so.6 for instance create a libstd++.so.5 as a > >> symbolic link. > >> 3) It's ok. > >> > >> -Original Message- > >> From: [EMAIL PROTECTED] > >> [mailto:[EMAIL PROTECTED] > >> mgh.harvard.edu] On Behalf Of ??? > >> Sent: quinta-feira, 4 de outubro de 2007 05:30 > >> To: freesurfer > >> Subject: [Freesurfer] problems > >> > >> Hi, > >> > >> I had downloaded the freesurfer to my system (Linux Fedora Core 4) > >> and had completed all the installation procedures. > >> > >> Question 1: > >> > >> I would like to convert analyze format to .mgz. What command line do I > >> use? > >> > >> Can I type "mri_convert x249.img 001.mgz "? > >> > >> > >> Question 2: > >> > >> When I type "recon-all -s x249 -nuintensitycor", it doesn't run and > >> has a error" nu_correct." What would I do to resolve the problem? > >> > >> > >> > >> Question 3: > >> > >> It doesn't find talairach.xfm. What would I do to get the file? > >> > >> thanks~~ > >> > >> > >> FreeSurfer problem report > >> > >> - > >> > >> FREESURFER_HOME: /usr/local/freesurfer > >> > >> Build stamp: freesurfer-Linux-centos4-stable-pub-v4.0.1 > >> > >> RedHat release: Fedora Core release 4 (Stentz) > >> > >> Kernel info: Linux 2.6.11-1.1369_FC4 i686 > >> > >> - > >> > >> > >> 1) subject name > >> x249 > >> 2) the entire command-line executed > >> > >>[EMAIL PROTECTED] ~]# ksh > >> # tcsh > >>[EMAIL PROTECTED] ~]# setenv FREESURFER_HOME > >> /usr/local/freesurfer > >>[EMAIL PROTECTED] ~]# source > >> $FREESURFER_HOME/SetUpFreeSurfer.csh > >> > >>[EMAIL PROTECTED] ~]# cd $SUBJECTS_DIR > >>[EMAIL PROTECTED] subjects]# cd x249/mri/orig > >>[EMAIL PROTECTED] orig]# mri_convert x249.img 001.mgz > >> > >>[EMAIL PROTECTED] mri]# recon-all -s x249 -nuintensitycor > >> > >> 3) the error message generated > >> > >> ERROR: nu_correct > >>
[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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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.mgh.harvard.edu/mailman/listinfo/freesurfer
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_convert x249.img 001.mgz > 2) It's missing libstd++.so.5. I suggest you run find / -name "libstd*" > -print > If you find a libstd++.so.6 for instance create a libstd++.so.5 as a > symbolic link. > 3) It's ok. > > -Original Message- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > mgh.harvard.edu] On Behalf Of ??? > Sent: quinta-feira, 4 de outubro de 2007 05:30 > To: freesurfer > Subject: [Freesurfer] problems > > Hi, > > I had downloaded the freesurfer to my system (Linux Fedora Core 4) > and had completed all the installation procedures. > > Question 1: > > I would like to convert analyze format to .mgz. What command line do I > use? > > Can I type "mri_convert x249.img 001.mgz "? > > > Question 2: > > When I type "recon-all -s x249 -nuintensitycor", it doesn't run and > has a error" nu_correct." What would I do to resolve the problem? > > > > Question 3: > > It doesn't find talairach.xfm. What would I do to get the file? > > thanks~~ > > > FreeSurfer problem report > > - > > FREESURFER_HOME: /usr/local/freesurfer > > Build stamp: freesurfer-Linux-centos4-stable-pub-v4.0.1 > > RedHat release: Fedora Core release 4 (Stentz) > > Kernel info: Linux 2.6.11-1.1369_FC4 i686 > > - > > > 1) subject name > x249 > 2) the entire command-line executed > >[EMAIL PROTECTED] ~]# ksh > # tcsh >[EMAIL PROTECTED] ~]# setenv FREESURFER_HOME /usr/local/freesurfer >[EMAIL PROTECTED] ~]# source $FREESURFER_HOME/SetUpFreeSurfer.csh > >[EMAIL PROTECTED] ~]# cd $SUBJECTS_DIR >[EMAIL PROTECTED] subjects]# cd x249/mri/orig >[EMAIL PROTECTED] orig]# mri_convert x249.img 001.mgz > >[EMAIL PROTECTED] mri]# recon-all -s x249 -nuintensitycor > > 3) the error message generated > > ERROR: nu_correct > > > 4) optionally include the subject's /script/recon-all.log > > > Thu Oct 4 13:38:14 CST 2007 > /usr/local/freesurfer/subjects/x249 > /usr/local/freesurfer/bin/recon-all > -s x249 -nuintensitycor > subjid x249 > setenv SUBJECTS_DIR /usr/local/freesurfer/subjects > FREESURFER_HOME /usr/local/freesurfer > Actual FREESURFER_HOME /usr/local/freesurfer > build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v4.0.1 > Linux cgu.edu.tw 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 > i686 i386 GNU/Linux > cputime unlimited > filesize unlimited > datasize unlimited > stacksize10240 kbytes > coredumpsize 0 kbytes > memoryuseunlimited > vmemoryuse unlimited > descriptors 1024 > memorylocked 32 kbytes > maxproc 16383 > > program versions used > $Id: recon-all,v 1.133.2.5 2007/09/17 16:38:00 nicks Exp $ > $Id: mri_motion_correct.fsl,v 1.7 2007/01/06 00:01:14 nicks Exp $ > mri_convert -all-info > ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: > $Name: stable4 $ TimeStamp: 2007/10/04-05:38:14-GMT BuildTimeStamp: > Sep 18 2007 04:54:49 CVS: $Id: mri_convert.c,v 1.146 2007/07/26 > 19:26:26 greve Exp $ User: root Machine: cgu.edu.tw Platform: Linux > PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC > CompilerVersion: 30400 > FLIRT version 5.4.2 > $Id: talairach_avi,v 1.4 2007/05/29 23:24:27 nicks Exp $ > mri_convert --version > stable4 > ProgramName: tkregister2_cmdl ProgramArguments: --all-info > ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:14-GMT > BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: tkregister2.c,v > 1.86.2.1 2007/08/15 15:39:42 nicks Exp $ User: root Machine: > cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 > CompilerName: GCC CompilerVersion: 30400 > Program nu_correct, built from: > Package MNI N3, version 1.10, compiled by [EMAIL PROTECTED] > (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 > ProgramName: mri_normalize ProgramArguments: -all-info > ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT > BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_normalize.c,v 1.52 > 2007/01/02 21:34:40 nicks Exp $ User: root Machine: cgu.edu.tw > Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC > CompilerVersion: 30400 > ProgramName: mri_watershed ProgramArguments: -all-info > ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT > BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_watershed.cpp,v > 1.67 2007/06/29 13:40:47 fischl Exp $ User: root Machine: cgu.edu.tw > Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: > GCC CompilerVersion: 30400 > ProgramName: m
