[christ21]

Thank you very much!

[christ21]

I could solve the problem. The file I am looking for is created when I start ‘generate_statistics_xls’ by using the commanding line.
However, thank you very much for your support and help!

[christ21]

I am sorry. Yes, I mean I am looking for 20150457.roiwise.stats.txt.

[christ21]

I tried it again. Unfortunately, again I could not find the file.

This is what I can find in the Brain Suite Log after running Cortical Surface Extraction and SVReg using gui. The nii-file is called ‘20150427’ and the folder I chosed to save the files to automatically is called ‘TEST’.

Welcome to BrainSuite15b (build #2364, built with Qt 5.4.2, compiled with MSVC2013 on Aug 10 2015)
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\BrainSuite15b
Using SVReg installed in directory C:\Program Files\BrainSuite15b\svreg
Loaded label description file: C:\Program Files\BrainSuite15b\labeldesc\brainsuite_labeldescriptions_14May2014.xml
Autosave Prefix is C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST/20150427
saved C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.mask.nii.gz
saved C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.bse.nii.gz
Skull Stripping took 0:10.680
wrote C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.skull.label.nii.gz
wrote C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.brain.dfs
wrote C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.inner_skull.dfs
wrote C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.outer_skull.dfs
wrote C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.scalp.dfs
Skull and Scalp Modeling took 0:16.872
wrote C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.bfc.nii.gz
Nonuniformity Correction took 0:50.944
wrote C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.pvc.label.nii.gz
wrote C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.pvc.frac.nii.gz
Tissue Classification took 0:11.350
wrote C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.hemi.label.nii.gz
wrote C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.cerebrum.mask.nii.gz
Cerebrum Labeling took 1:18.457
Inner Cortical Mask took 0:02.698
wrote C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.cortex.scrubbed.mask.nii.gz
Scrub Mask took 0:03.274
wrote C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.cortex.tca.mask.nii.gz
Topology Correction took 3:19.224
wrote C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.cortex.dewisp.mask.nii.gz
Wisp Removal took 0:46.601
wrote C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.inner.cortex.dfs
Inner Cortical Surface took 0:02.528
copied cerebrum mask to displayed mask
using cerebrum mask to constrain surface expansion.
Completed pial surface generation.
wrote C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.pial.cortex.dfs
Pial Surface took 62:36.105
wrote C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.right.inner.cortex.dfs
wrote C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.left.inner.cortex.dfs
wrote C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.right.pial.cortex.dfs
wrote C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.left.pial.cortex.dfs
Split Hemispheres took 0:01.969
Using Autosave Prefix:C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427
Finished file preparation 0.003
Executing: C:\Program Files\BrainSuite15b\svreg\bin\svreg_label_surf_hemi.exe C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427 C:\Program Files\BrainSuite15b\svreg\BrainSuiteAtlas1\mri left -v1
Executing: C:\Program Files\BrainSuite15b\svreg\bin\svreg_label_surf_hemi.exe C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427 C:\Program Files\BrainSuite15b\svreg\BrainSuiteAtlas1\mri right -v1
Finished surface labeling 28:18
Executing: C:\Program Files\BrainSuite15b\svreg\bin\volmap_ball.exe C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427 1 -v1
Executing: C:\Program Files\BrainSuite15b\svreg\bin\volmap_ball.exe C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.target 1 -v1
Finished volume mapping 20:00
Executing: C:\Program Files\BrainSuite15b\svreg\bin\svreg_volreg.exe C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427 C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.target -v1
Finished volume registration 710:39
Executing: C:\Program Files\BrainSuite15b\svreg\bin\refine_ROIs2.exe C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427 left -v1
Executing: C:\Program Files\BrainSuite15b\svreg\bin\refine_ROIs2.exe C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427 right -v1
Finished refining surface labels 17:44
Executing: C:\Program Files\BrainSuite15b\svreg\bin\svreg_refinements.exe C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427 C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427.target -v1
Finished volume labeling refinement 29:23
Executing: C:\Program Files\BrainSuite15b\svreg\bin\generate_stats_xls.exe C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427 -r
Executing: C:\Program Files\BrainSuite15b\svreg\bin\clean_intermediate_files.exe C:\Users\Christian\Documents\Doktorarbeit\MRT\TEST\20150427
Register and Label Brain took 806:48.860
sequence took 876:29.563

There is no warning that SVReg has not worked properly. After SVReg has finished the Cortical Extraction Sequence Window ist still open. It says ‘finished registration and labeling’ and 100% are achieved.
When I use gui I can choose the folder to which the files are saved to automatically. I can find all the outputs of Cortical Surface Extraction and SVReg in the selected folder called ‘Test’ after the SVReg has completed but not the file ‘fileprefix.roiwise.stats.txt’. The Windows Explorer doesn’t find the file in any other folder of my PC.
Thank you very much for your help!

[christ21]

Dear Anand,
thank you very much for your quick answer!
I am checking the folder to which I saved the files created by Cortical Surface Extraction and SVReg using the GUI. The folder therefore contains the following files:
the nii-file
fileprefix.bse.nii
“.mask.nii
“.bfc.nii
“.brain
“.cerbrum.mask.nii
“.cortex.dewisp.mask.nii
“.cortex.scrubbed.mask.nii
“.cortex.tca.mask.nii
“.hemi.label.nii
“.init.cortex.mask.nii
“.inner.cortex
“.inner_skull
“.left.inner.cortex
“.left.mapped.dfc
“.left.mid.cortex.svreg.init
“.left.pial.cortex
“.mask.nii
“.outer_skull
“.pial.cortex
“.pvc.frac.nii
“.pvc.label.nii
“.right.inner.cortex
“.right.mapped.dfc
“.right.mid.cortex.svreg.init
“.right.pial.cortex
“.scalp
“.skull.label.nii
brainsuite_labeldescription

Furthermore, the folder contains the folder fileprefix.svreg.tmp. In this folder I also could not find the file ‘fileprefix.roiwise.stats.txt’
I use Brain Suite 15b and installed Matlab Runtime R2012a. My PC runs Windows 7.
I didn’t notice any error. I also tried it several times on another Windows PC with different nii-files. Again, I could not find the file.
Is this file created automatically by SVReg using the GUI or do I have to do anything special to have it created?
Thank you very much for your help!
Kind regards,
Christian

[christ21]

I have the same problem like Luca. As soon as I press on “open volume” or “save volume” BS does not work any more. It is only possible to open the file by using the Windows Explorer.
I also use NIFTI format and have tried several versions of BS.

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