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abhinavdhereParticipant
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.
abhinavdhereParticipantThanks 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 nonowner and nongroup member, you lack write permission for the specified file or directory. (AIR_WORLD_CANT_WRITE_ERROR)
As nonowner and nongroup 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 021101301 USA
Performing L2 registration
L2 distance minimization started. This can take 1015 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 registrationThe 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 = 0/262144The 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 = 0/262144The 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 = 0/262144The 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 nonowner and nongroup member, you lack write permission for the specified file or directory. (AIR_WORLD_CANT_WRITE_ERROR)
As nonowner and nongroup 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.
abhinavdhereParticipantDear 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. 
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