BrainSuite

Registration Process error

Viewing 8 reply threads
  • Author
    Posts
    • 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 8 years, 12 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)

                    • Author
                      Posts
                    Viewing 8 reply threads
                    • You must be logged in to reply to this topic.