abhinavdhere

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  • in reply to: registration process error #1131
    abhinavdhere
    Participant

    Thanks a lot for your time. I resolved that issue myself.
    It seems the problem was that I was trying to do the SVreg process directly on pial surface, without hemisphere labeling. Performing hemisphere labeling step before registration resolved the issue.

    Now I have the labeled surface with the 95 ROIs color coded. However, I’m not sure how to visualize any sulcal markings (the atlas description has 26 sulci). My primary motive here was to obtain automatic marking of those 26 sulci on the surface.

    in reply to: registration process error #1118
    abhinavdhere
    Participant

    Thanks for quick response. The log is as follows:

    left log:
    —–
    Labeling left hemisphere
    Computing mid cortical surfaces
    Checking Euler Characteristic of input surfaces, it should be 1
    Euler characteristic of left Hemi = 1
    Computing Smooth cortical representation
    Generating Smooth representations of the surface
    Performing L2 registration and flattening
    Computing faces and vertices connectivity
    Applying deformation field from AIR
    Pausing for 5 sec. to clear file buffers
    ans =
    1
    Using Executable /home/abhinav/BrainSuite17a/svreg/bin/warp_points_linux
    As non-owner and non-group member, you lack write permission for the specified file or directory. (AIR_WORLD_CANT_WRITE_ERROR)
    As non-owner and non-group member, you lack write permission for the specified file or directory. (AIR_WORLD_CANT_WRITE_ERROR)
    Registering corpus callosum curve
    ans =
    1
    The register_cc_curve program as a part of the RCC package is provided under the terms
    of the GNU General Public License, version 2 as published by
    the Free Software Foundation.
    RCC is based on Coherent Point Drift (CPD) Package provided from
    https://sites.google.com/site/myronenko/research/cpd
    RCC package is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
    GNU General Public License for more details.
    You should have received a copy of the GNU General Public License
    along with RCC package; if not, write to the Free Software
    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
    Performing L2 registration
    L2 distance minimization started. This can take 10-15 min.
    L2 distance minimization is done
    Mapping to unit square
    Performing curvature registration
    Calculating Multiresolution curvature maps
    Multiresolution curvature maps are calculated
    Computing additive curvature
    Performing curvature registration

    The Laplacian matrix takes 23035912 bytes

    linesearch step too small
    iter 1/50 f = 50.7582, linesearch iter=39
    iter 2/50 f = 295.532, linesearch iter=4
    iter 3/50 f = 289.286, linesearch iter=10
    iter 4/50 f = 286.968, linesearch iter=6
    iter 5/50 f = 278.225, linesearch iter=9
    iter 6/50 f = 276.886, linesearch iter=11
    iter 7/50 f = 276.864, linesearch iter=12
    iter 8/50 f = 276.647, linesearch iter=13
    iter 9/50 f = 276.647, linesearch iter=13
    iter 10/50 f = 276.647, linesearch iter=14
    iter 11/50 f = 276.647, linesearch iter=17
    iter 12/50 f = 276.647, linesearch iter=17
    iter 13/50 f = 276.647, linesearch iter=17
    iter 14/50 f = 276.647, linesearch iter=19
    Negative Jacobians in surf reg step = 0/262144

    The Laplacian matrix takes 23035912 bytes

    linesearch step too small
    iter 1/50 f = 170.919, linesearch iter=37
    iter 2/50 f = 322.2, linesearch iter=4
    iter 3/50 f = 313.142, linesearch iter=9
    iter 4/50 f = 305.543, linesearch iter=7
    iter 5/50 f = 300.156, linesearch iter=8
    iter 6/50 f = 299.671, linesearch iter=10
    iter 7/50 f = 299.671, linesearch iter=13
    iter 8/50 f = 299.671, linesearch iter=13
    iter 9/50 f = 299.671, linesearch iter=15
    iter 10/50 f = 299.671, linesearch iter=16
    iter 11/50 f = 299.671, linesearch iter=17
    Negative Jacobians in surf reg step = 0/262144

    The Laplacian matrix takes 23035912 bytes

    linesearch step too small
    iter 1/50 f = 275.207, linesearch iter=36
    iter 2/50 f = 429.659, linesearch iter=3
    iter 3/50 f = 402.783, linesearch iter=12
    iter 4/50 f = 400.133, linesearch iter=8
    iter 5/50 f = 399.817, linesearch iter=10
    iter 6/50 f = 399.792, linesearch iter=10
    iter 7/50 f = 399.767, linesearch iter=12
    iter 8/50 f = 399.764, linesearch iter=12
    iter 9/50 f = 399.762, linesearch iter=13
    iter 10/50 f = 399.761, linesearch iter=13
    iter 11/50 f = 399.761, linesearch iter=14
    iter 12/50 f = 399.76, linesearch iter=14
    iter 13/50 f = 399.76, linesearch iter=14
    iter 14/50 f = 399.76, linesearch iter=15
    iter 15/50 f = 399.76, linesearch iter=18
    iter 16/50 f = 399.76, linesearch iter=18
    iter 17/50 f = 399.76, linesearch iter=19
    iter 18/50 f = 399.76, linesearch iter=19
    Negative Jacobians in surf reg step = 0/262144

    The Laplacian matrix takes 23035912 bytes

    linesearch step too small
    iter 1/50 f = 386.463, linesearch iter=35
    iter 2/50 f = 526.192, linesearch iter=3
    iter 3/50 f = 488.092, linesearch iter=14
    iter 4/50 f = 487.941, linesearch iter=11
    iter 5/50 f = 487.93, linesearch iter=12
    iter 6/50 f = 487.926, linesearch iter=14
    iter 7/50 f = 487.926, linesearch iter=15
    iter 8/50 f = 487.926, linesearch iter=16
    iter 9/50 f = 487.926, linesearch iter=18
    iter 10/50 f = 487.926, linesearch iter=18
    iter 11/50 f = 487.926, linesearch iter=18
    Negative Jacobians in surf reg step = 0/262144
    Curvature registration done.
    Transferring Labels
    left hemisphere done
    Transferring Curves
    Labeling of a hemisphere is done!

    right log:
    —–
    Labeling right hemisphere
    Computing mid cortical surfaces
    Checking Euler Characteristic of input surfaces, it should be 1
    Euler characteristic of right Hemi = 1
    Computing Smooth cortical representation
    Generating Smooth representations of the surface
    Performing L2 registration and flattening
    Computing faces and vertices connectivity
    Applying deformation field from AIR
    Pausing for 5 sec. to clear file buffers
    ans =
    1
    Using Executable /home/abhinav/BrainSuite17a/svreg/bin/warp_points_linux
    As non-owner and non-group member, you lack write permission for the specified file or directory. (AIR_WORLD_CANT_WRITE_ERROR)
    As non-owner and non-group member, you lack write permission for the specified file or directory. (AIR_WORLD_CANT_WRITE_ERROR)
    SVREG Warning: .warp file was not in correct format. Continuing after trying to fix.
    Error using readdfs (line 61)
    Unable to read:/home/abhinav/somePath/CAHI01M.svreg.tmp/CAHI01M.target.right.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)

    Pls. note that this is despite the fact that I have run the program as sudo and have ensured that mri.warp is allowed to execute as program and access is read only to others, read and write to user.

    in reply to: registration process error #1116
    abhinavdhere
    Participant

    Dear Prof. Joshi,
    Both the BrainSuite software and SVreg are useful tools. However, I am facing the exactly same issue as faced by yunliaoyu, but for 64 bit Linux (Ubuntu 16.04) and BrainSuite 17a. Naturally the Visual Studio fix doesn’t seem useful in this case.
    Kindly suggest if there is a fix available for Linux also?
    Thanks.

Viewing 3 posts - 1 through 3 (of 3 total)