Re: [Freesurfer] ascii file

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 <fischl@nmr.mgh.harvard.edu mailto:fischl@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

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