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# average cortical thickness of ROI

• Author
Posts
• #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,
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
“.bfc.nii
“.brain
“.hemi.label.nii
“.inner.cortex
“.inner_skull
“.left.inner.cortex
“.left.mapped.dfc
“.left.mid.cortex.svreg.init
“.left.pial.cortex
“.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 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.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
Cerebrum Labeling took 1:18.457
Topology Correction took 3:19.224
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
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.