christ21

Forum Replies Created

Viewing 6 posts - 1 through 6 (of 6 total)
  • Author
    Posts
  • in reply to: average cortical thickness of ROI #186
    christ21
    Participant

    Thank you very much!

    in reply to: average cortical thickness of ROI #184
    christ21
    Participant

    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!

    in reply to: average cortical thickness of ROI #183
    christ21
    Participant

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

    in reply to: average cortical thickness of ROI #181
    christ21
    Participant

    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!

    in reply to: average cortical thickness of ROI #169
    christ21
    Participant

    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

    in reply to: installation problems #164
    christ21
    Participant

    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.

Viewing 6 posts - 1 through 6 (of 6 total)