BrainSuite

Registration Process error

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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, 5 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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