Registration Process error

This topic has 8 replies, 2 voices, and was last updated 7 years, 10 months ago by Anand Joshi.

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- October 31, 2016 at 10:09 pm #558
  
  tooba altaf
  Participant
  
  hello
  while using Surface and Volume registration , i get following errors and i am not able to figure out what is wrong . will u please guide me .
  below is my error which i got when i run SVreg
  
  Error running surface labeling. Processing halted.
  left log:
  —–
  Labeling left hemisphere
  Error using copyfile
  The system cannot find the path specified.
  
  Error in svreg_label_surf_hemi (line 93)
  
  MATLAB:COPYFILE:OSError
  
  right log:
  —–
  Labeling right hemisphere
  Error using copyfile
  The system cannot find the path specified.
  
  Error in svreg_label_surf_hemi (line 93)
  
  MATLAB:COPYFILE:OSError
  
  Register and Label Brain took 2:40.935
  sequence took 29:10.375
- November 1, 2016 at 2:20 pm #559
  
  Anand Joshi
  Moderator
  
  Hi – Can you send me or post here the log file> There should be a subj_name.svreg.log file in the subject folder or in the sub_name/sub_name.svreg.tmp folder.
- November 1, 2016 at 8:21 pm #561
  tooba altaf
  Participant
  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 C:\Users\tooba\Desktop\checking brain suit/ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108
  saved C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108.mask.nii.gz
  saved C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108.bse.nii.gz
  Skull Stripping took 0:03.289
  wrote C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108.skull.label.nii.gz
  wrote C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108.brain.dfs
  wrote C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108.inner_skull.dfs
  wrote C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108.outer_skull.dfs
  wrote C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108.scalp.dfs
  Skull and Scalp Modeling took 0:04.592
  wrote C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108.bfc.nii.gz
  Nonuniformity Correction took 0:19.572
  wrote C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108.pvc.label.nii.gz
  wrote C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108.pvc.frac.nii.gz
  Tissue Classification took 0:03.870
  running align linear
  ..\libraries\AIR5.3.0\src\align.c: 518: WARNING: Registration terminated due to a Hessian matrix that was not positive definite
  Inspection of results is advised
  finished align linear 0:10
  running align warp
  Performing warp alignment (order=5) of atlas brain to subject brain
  ..\libraries\AIR5.3.0\src\alignwarp.c: 262: WARNING: Registration terminated due to a Hessian matrix that was not positive definite
  Inspection of results is advised
  finished align warp 0:05
  wrote C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108.hemi.label.nii.gz
  wrote C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108.cerebrum.mask.nii.gz
  Cerebrum Labeling took 0:17.225
  Inner Cortical Mask took 0:01.029
  wrote C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108.cortex.scrubbed.mask.nii.gz
  Scrub Mask took 0:00.783
  wrote C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108.cortex.tca.mask.nii.gz
  Topology Correction took 3:14.883
  wrote C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108.cortex.dewisp.mask.nii.gz
  Wisp Removal took 0:12.686
  wrote C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108.inner.cortex.dfs
  Inner Cortical Surface took 0:01.218
  copied cerebrum mask to displayed mask
  using cerebrum mask to constrain surface expansion.
  Completed pial surface generation.
  wrote C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108.pial.cortex.dfs
  Pial Surface took 15:00.801
  wrote C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108.right.inner.cortex.dfs
  wrote C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108.left.inner.cortex.dfs
  wrote C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108.right.pial.cortex.dfs
  wrote C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108.left.pial.cortex.dfs
  Split Hemispheres took 0:01.818
  Using Autosave Prefix:C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108
  Finished file preparation 0.003
  Executing: C:\Program Files\BrainSuite16a1\svreg\bin\svreg_label_surf_hemi.exe C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108 C:\Program Files\BrainSuite16a1\svreg\BCI-DNI_brain_atlas\BCI-DNI_brain left -v1
  Executing: C:\Program Files\BrainSuite16a1\svreg\bin\svreg_label_surf_hemi.exe C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108 C:\Program Files\BrainSuite16a1\svreg\BCI-DNI_brain_atlas\BCI-DNI_brain right -v1
  Error running surface labeling. Processing halted.
  left log:
  —–
  Labeling left hemisphere
  Error using copyfile
  The system cannot find the path specified.
  
  Error in svreg_label_surf_hemi (line 93)
  
  MATLAB:COPYFILE:OSError
  
  right log:
  —–
  Labeling right hemisphere
  Error using copyfile
  The system cannot find the path specified.
  
  Error in svreg_label_surf_hemi (line 93)
  
  MATLAB:COPYFILE:OSError
  
  Register and Label Brain took 8:19.431
  sequence took 27:41.226
  - This reply was modified 7 years, 11 months ago by tooba altaf.
- November 1, 2016 at 8:24 pm #562
  
  tooba altaf
  Participant
  
  here is the log file
  
  SVREG Version 16a(build#2234) (svreg_label_surf_hemi)
  svreg_label_surf_hemi C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108 C:\Program Files\BrainSuite16a1\svreg\BCI-DNI_brain_atlas\BCI-DNI_brain right -v1
  SVREG Version 16a(build#2234) (svreg_label_surf_hemi)
  svreg_label_surf_hemi C:\Users\tooba\Desktop\checking brain suit\ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_Br_20070319113623975_S13408_I45108 C:\Program Files\BrainSuite16a1\svreg\BCI-DNI_brain_atlas\BCI-DNI_brain left -v1
- November 1, 2016 at 11:14 pm #564
  
  Anand Joshi
  Moderator
  
  Thank you for reporting the error. Can you try deleting the spaces in directory name ‘checking brain suite’? Also, have you tried the tutorial data? http://brainsuite.org/tutorials/cseexcercise/
  If not I suggest trying that first to make sure that your brainsuite setup is correct.
- November 2, 2016 at 3:19 am #565
  
  tooba altaf
  Participant
  
  i have remove the space also i check the setup its correct ,but my issue is still there.
- November 22, 2016 at 2:57 pm #582
  
  Anand Joshi
  Moderator
  
  Does the following directory exist on your system? C:\Program Files\BrainSuite16a1\svreg\BCI-DNI_brain_atlas
  This directory should have the following two files. Please check and let me know,
  BCI-DNI_brain.left.mid.cortex.dfs
  BCI-DNI_brain.right.mid.cortex.dfs
  thanks,
- November 28, 2016 at 9:33 pm #595
  
  tooba altaf
  Participant
  
  yes i have both in my system
- November 28, 2016 at 9:43 pm #596
  
  Anand Joshi
  Moderator
  
  Hi Tooba,
  
  Thank you for checking this out. Do you get this error every time you run BrainSuite on this or some other subject? If yes then I suggest trying the tutorial dataset mentioned in my earlier post to make sure that your BrainSuite setup is correct. Please let me know how it goes.
  Anand
- February 28, 2020 at 2:07 am #2147
  
  Gaoming
  Participant
  
  Hello
  while using Surface and Volume registration , I get following errors and i am not able to figure out what is wrong . will you please guide me .
  below is my error which i got when i run SVreg
  
  Label Cerebral Hemisphere Surfaces
  Error in svreg_label_surf_hemi (line 163)
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Registration Process error

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