Registration Process Error

Forums Forums Surface and Volume Registration (SVReg) Registration Process Error

This topic contains 6 replies, has 2 voices, and was last updated by  Anand Joshi 3 months, 2 weeks ago.

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  • #1239

    wy
    Participant

    Had this error after while trying to register.
    could not launch Label Left Hemisphere Surface please check that the executable /Applications/BrainSuite18a/svreg/bin/svreg_label_surf_hemi.sh exists and that /Users/walidyassine/Documents/Todai/Studies/VoiceTask_study/BS_SPGR/A02 is a valid directory.

    I checked both, and both are fine!
    Any advice what to do next?

  • #1240

    wy
    Participant

    Any help?

  • #1241

    wy
    Participant

    How do i delete this post? Just saw that i already asked this few month back and got no answer!

  • #1242

    wy
    Participant

    an*

  • #1254

    Anand Joshi
    Moderator

    Hi Wy, I will try to help you with this.
    Can you try running /Applications/BrainSuite18a/svreg/bin/svreg_label_surf_hemi.sh
    from the command line and let me know what message you get?

  • #1259

    wy
    Participant

    Thank you very much.

    Here is the output.

    surface registration and labeling (svreg)
    This is the main program for surface registration. First, the surface is
    smoothed to create a multiresolution representation of the surface. An
    initial registration is performed by aligning the 3D coordinates of this
    smoothed surface. This is followed by p-harmonic mapping to a square and
    curvature-based registration.
    For more information, please see http://brainsuite.org
    Authored by Anand A. Joshi, Signal and Image Processing Institute
    Department of Electrical Engineering, Viterbi School of Engineering, USC

    usage: svreg_label_surf_hemi.sh [subject fileprefix] [atlas fileprefix]
    [hemi] [flags]

    required input:
    subject fileprefix path and filename prefix of the subject’s output
    from BrainSuite’s Cortical Surface Extraction
    Sequence
    atlas fileprefix path and filename prefix of atlas files and labels
    to which the subject will be registered
    hemi the hemisphere to refine; either left or right

    optional flags:
    -v# Controls the verbosity of output messages (# is 0, 1, or 2)
    -t display timestamps along with output messages

    Here is one of the errors i am getting from the run..

    Using Executable /Applications/BrainSuite18a/svreg/bin/warp_points_mac
    A matrix with a negative or zero determinant was encountered. (AIR_NON_POSITIVE_DETERMINANT_ERROR)
    SVREG Warning: .warp file was not in correct format. Continuing after trying to fix.
    Error using readdfs (line 61)
    Unable to read:~/study/BS_SPGR/A11/A11.svreg.tmp/A11.target.left.mid.cortex_smooth10_smooth10.dfs
    Error in surf_align_autocorrect_with_AIR (line 159)
    Error in align_surf_curves (line 62)
    Error in surf_flatten_newbs (line 32)
    Error in svreg_label_surf_hemi (line 163)

    another is the pial line. While brainsuite is running, i can see that it was too much inside the brain, sometimes including the inner temporal!!!

  • #1260

    Anand Joshi
    Moderator

    Ok thanks. From the BrainSuite GUI, goto Cortex->Select SVReg directory.
    Then from the dialog box, goto BrainSuite installation folder and select directory named svreg.
    After this, try running the whole sequence for your subject data and it should work.

    The next error is something else. It is due to some errors in surface extraction. Please make sure that the cortical surface you get look reasonable, as shown on brainsuite website.

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