[yunliaoyu]

Hello:
I encountered an error during register and label brain process.It seems like .warp file cannot be read.I have tried many ways but still cannot fix it. Would you please help me to know what is wrong? Thanks! BTW, I use windows and I am sure that MATLAB MCR is installed.

Following is the detailed Brainsuite log:
Welcome to BrainSuite16a1 (build #2777, built with Qt 5.6.1, compiled with MSVC2013 on Sep 15 2016)
Copyright (C) 2016 The Regents of the University of California
This program is free software and is released under a GNU General Public License; Version 2. For more details, please see the enclosed license files.
BrainSuite uses the Qt GUI Toolkit. The Qt GUI Toolkit is Copyright (C) 2015 Digia Plc and/or its subsidiary(-ies) and is licensed under the LGPL v2.1.
BrainSuite install directory: C:\Program Files\BrainSuite16a1
Using SVReg installed in directory C:\Program Files\BrainSuite16a1\svreg
Autosave Prefix is F:\wangxu\mri_bs_test/T1.bfc
Using Autosave Prefix:F:\wangxu\mri_bs_test\T1.bfc
Finished file preparation 0.000
Executing: C:\Program Files\BrainSuite16a1\svreg\bin\svreg_label_surf_hemi.exe F:\wangxu\mri_bs_test\T1.bfc C:\Program Files\BrainSuite16a1\svreg\BrainSuiteAtlas1\mri left -v1
Executing: C:\Program Files\BrainSuite16a1\svreg\bin\svreg_label_surf_hemi.exe F:\wangxu\mri_bs_test\T1.bfc C:\Program Files\BrainSuite16a1\svreg\BrainSuiteAtlas1\mri right -v1
Error running surface labeling. Processing halted.
left log:
—–
Labeling left hemisphere
Computing mid cortical surfaces
Checking Euler Characteristic of input surfaces, it should be 1
Euler characteristic of left Hemi = 9
New Euler characteristic of left Hemi = -2
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
Using Executable C:\Program Files\BrainSuite16a1\svreg\bin\warp_points.exe
SVREG Warning: .warp file was not in correct format. Continuing after trying to fix.
Error using readdfs (line 61)
Unable to read:F:\wangxu\mri_bs_test\T1.bfc.svreg.tmp\T1.bfc.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 164)

right log:
—–
Labeling right hemisphere
Computing mid cortical surfaces
Checking Euler Characteristic of input surfaces, it should be 1
Euler characteristic of right Hemi = -10
New Euler characteristic of right Hemi = -12
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
Using Executable C:\Program Files\BrainSuite16a1\svreg\bin\warp_points.exe
SVREG Warning: .warp file was not in correct format. Continuing after trying to fix.
Error using readdfs (line 61)
Unable to read:F:\wangxu\mri_bs_test\T1.bfc.svreg.tmp\T1.bfc.right.mid.cortex_smooth10_smooth10.dfs

Error in surf_align_autocorrect_with_AIR (line 160)

Error in align_surf_curves (line 62)

Error in surf_flatten_newbs (line 32)

Error in svreg_label_surf_hemi (line 164)

Register and Label Brain took 1:08.308

It will help a lot if you reply.Thanks!

XU WANG

[Anand Joshi]

Is there a file F:\wangxu\mri_bs_test\T1.bfc.warp ?

[yunliaoyu]

yes，I have that file.

[Anand Joshi]

Hi Xu, Is your data on external hard drive? If yes then can you please try copying it on internal drive and then running the program? The speed of the external drive may not be enough for data processing. Please let me know.

[yunliaoyu]

Hi,The data I processed is on the internal drive. I checked the log again and found that I only have F:\wangxu\mri_bs_test\T1.bfc.svreg.tmp\T1.bfc.target.left.mid.cortex_smooth10.dfs. But the file that mentioned in the log is F:\wangxu\mri_bs_test\T1.bfc.svreg.tmp\T1.bfc.target.left.mid.cortex_smooth10_smooth10.dfs. Is it the problem? Looking forward to your reply! Thanks!

[Anand Joshi]

Can you try running the surface extraction sequence again? My guess is that for some reason .warp file is corrupted leading to the error in later stages. If it is possible for you to share the data with me, I can try running it.

[yunliaoyu]

I have tried running the extract sequence again and using another file, but still encountered this error. Of course I can share my data with you. It is of great help if you run it. Would you please tell me your email? Thanks!

[Anand Joshi]

My email ID is ajoshi@sipi.usc.edu. You are using 64 bit windows platform, right?

[yunliaoyu]

Yes, I used 64 bit windows platform. I sent a file I used in this process to you by E-mail. Thanks for your help!

[Anand Joshi]

I am not able to find your email. What was the subject or email address from which you sent it?

[yunliaoyu]

maybe some error occurred in my mail system. I resent you a E-mail. The subject is ‘nii file for running cortical surface extraction sequence’ and my E-mail address is wangxu2011@sjtu.edu.cn

[tenamber]

Hey, I experience the exact same Problem.
Has this been solved somehow?
Thanks, Frederik

[Anand Joshi]

Hi, Thank you for reporting the issue.
Are you able to run the following exe from the command line
> C:\Program Files\BrainSuite16a1\svreg\bin\warp_points.exe

It should show the following message.
> C:\Users\ajoshi>”C:\Program Files\BrainSuite16a1\svreg\bin\warp_points.exe”
>
> Usage: C:\Program Files\BrainSuite16a1\svreg\bin\warp_points.exe .warp_file ucf_in ucf_out

Please let me know what message you get.
Additionally, please make sure that your windows system is up to date with all the updates applied.
Can you please report your windows system configuration?
Thanks,
Anand

• This reply was modified 8 years ago by Anand Joshi. Reason: updates
• This reply was modified 8 years ago by Anand Joshi.

[Anand Joshi]

A possible fix it installing 32 bit redistributable from:
https://www.microsoft.com/en-us/download/details.aspx?id=40784
Make sure to install 32bit version of Visual C++ Redistributable Packages for Visual Studio 2013.

[gee306]

After installed the 32bit version of Visual C++ Redistributable Packages

I have already solve the same problem.

It has bothered me a long time.

Thanks Anand Joshi !

[abhinavdhere]

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.

[Anand Joshi]

Can you please type the error log here?

[abhinavdhere]

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.

[abhinavdhere]

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.

[Anand Joshi]

You can drag and drop dfc files in brainsuite interface to see the sulci.

[Renatar]

Hi, I have the same issue. Something is wrong with the warp_points.exe file. The program just stops to work with “Registration error” message. The log is:

Welcome to BrainSuite18a (build #3115, built with Qt 5.6.3, compiled with MSVC2015 on Feb 28 2018)
Copyright (C) 2018 The Regents of the University of California
This program is free software and is released under a GNU General Public License; Version 2. For more details, please see the enclosed license files.
BrainSuite uses the Qt GUI Toolkit. The Qt GUI Toolkit is Copyright (C) 2015 Digia Plc and/or its subsidiary(-ies) and is licensed under the LGPL v2.1.
BrainSuite install directory: C:\Program Files\BrainSuite18a
Using SVReg installed in directory C:\Program Files\BrainSuite18a\svreg
Finished file preparation 0.000
Executing: C:\Program Files\BrainSuite18a\svreg\bin\svreg_label_surf_hemi.exe D:\ADMI\BrainSuite\tests\d\IXI603-HH-2701-T1 C:\Program Files\BrainSuite18a\svreg\BrainSuiteAtlas1\mri left -v1
Executing: C:\Program Files\BrainSuite18a\svreg\bin\svreg_label_surf_hemi.exe D:\ADMI\BrainSuite\tests\d\IXI603-HH-2701-T1 C:\Program Files\BrainSuite18a\svreg\BrainSuiteAtlas1\mri right -v1
Error running surface labeling. Processing halted.
left log:
—–
Labeling left hemisphere
Computing mid cortical surfaces
Checking Euler Characteristic of input surfaces, it should be 1
Euler characteristic of left Hemi = -3
New Euler characteristic of left Hemi = -3
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
Using Executable C:\Program Files\BrainSuite18a\svreg\bin\warp_points.exe
SVREG Warning: .warp file was not in correct format. Continuing after trying to fix.
Error using readdfs (line 61)
Unable to read:D:\ADMI\BrainSuite\tests\d\IXI603-HH-2701-T1.svreg.tmp\IXI603-HH-2701-T1.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)

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
Using Executable C:\Program Files\BrainSuite18a\svreg\bin\warp_points.exe
SVREG Warning: .warp file was not in correct format. Continuing after trying to fix.
Error using readdfs (line 61)
Unable to read:D:\ADMI\BrainSuite\tests\d\IXI603-HH-2701-T1.svreg.tmp\IXI603-HH-2701-T1.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)

[Anand Joshi]

Is your windows system 32 bit o 64 bit?
Is the pial surface generated correctly?

[Anand Joshi]

Please try installing
Visual C++ Redistributable Packages for Visual Studio 2013

available from
https://www.microsoft.com/en-us/download/details.aspx?id=40784

Make sure to get

vcredist_x64.exe

After this the programs should work.

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