average cortical thickness of ROI

Forums Forums Surface and Volume Registration (SVReg) average cortical thickness of ROI

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    • #167
      christ21
      Participant

      Dear all,
      I have been using Brain Suite for two weeks and I really like it.
      Unfortunately, I can’t find a file which should be created by SVReg according to the software description. I would be very glad if someone could help me!
      By using Matlab, I was able to read vertex-wise cortical thickness. In fact, I am more interested in the average cortical thickness of labeled structure. The description of the output of SVReg says that there is a file called ‘fileprefix.roiwise.stats.txt’ which contains the volume and (where applicable) average cortical thickness of labeled structure. However, I am not able to find this file in the folder containing the SVReg outputs. I have tried SVReg several times. How can I create the file ‘fileprefix.roiwise.stats.txt’?
      Thank you very much for your help!

    • #168
      Anand Joshi
      Moderator

      The file should have been generated. Which folder are you checking and can you please give me a list of files that are generated? Can you please give more information about version and platform that you are using? Also did you notice any error during the processing, did the sequence finish successfully?

    • #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

      • #171
        Anand Joshi
        Moderator

        Based on this, I think the SVReg sequence has not finished. There must be error. If you can try again and send us a screenshot of when the sequence stops, that will be helpful. When the SVReg sequence finishes (cmd line or gui) it generates the following outputs. SVReg generally takes 1-2 hrs.
        http://brainsuite.org/processing/svreg/output/

    • #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!

      • #182
        Anand Joshi
        Moderator

        The file you are looking for is 20150427.roiwise.stats.txt right? fileprefix should be replaced by name of the subject. I am asking just to be sure.

    • #183
      christ21
      Participant

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

    • #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!

    • #185
      Anand Joshi
      Moderator

      Great! We will check if there is any issue in generating this file when the sequence is run through the gui and fix it. Thank you for reporting.

    • #186
      christ21
      Participant

      Thank you very much!

      • #187
        Anand Joshi
        Moderator

        I tried it now but the stats.txt file was generated as expected. We will investigate it if we can reproduce the issue or if it reoccurs. Glad that things are working for you now.

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