- This topic has 8 replies, 2 voices, and was last updated 8 years ago by Anand Joshi.
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October 31, 2016 at 10:09 pm #558tooba altafParticipant
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 SVregError running surface labeling. Processing halted.
left log:
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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:
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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 #559Anand JoshiModerator
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.
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November 1, 2016 at 8:21 pm #561tooba altafParticipant
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:
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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, 1 month ago by tooba altaf.
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November 1, 2016 at 8:24 pm #562tooba altafParticipant
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 #564Anand JoshiModerator
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 #565tooba altafParticipant
i have remove the space also i check the setup its correct ,but my issue is still there.
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November 22, 2016 at 2:57 pm #582Anand JoshiModerator
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 #595tooba altafParticipant
yes i have both in my system
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November 28, 2016 at 9:43 pm #596Anand JoshiModerator
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 #2147GaomingParticipant
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 SVregLabel Cerebral Hemisphere Surfaces
Error in svreg_label_surf_hemi (line 163)
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