[Anand Joshi]

Hi Lenia, Sorry for the delay in getting back to you on this. The ROIs are generated by SVReg module in BrainSuite. The output file names are defined here:
http://brainsuite.org/processing/svreg/output/

Anand

[Anand Joshi]

For tractography and finding connectivity across regions, we do not need AC PC alignment in BrainSuite.
http://brainsuite.org/processing/diffusion/tractography/

[Anand Joshi]

It should take 2-3 hrs for BrainSuite+SvReg on normal brains if there is sufficient memory and processing power available. Please make sure that there is >=4GB RAM free when you are running the software. For this purpose, closing as many programs as possible is helpful. Also make sure that hibernation or sleep modes are disabled.

[Anand Joshi]

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

[Anand Joshi]

Hi lena, Thank you for using BrainSuite.
1. The ROIs generated by BrainSuite are in the native coordinates of the subject. This is because BrainSuite and SVReg warp atlas to match the subject and transfer the ROIs from the atlas to subject.
2. It is possible to edit the ROIs generated by BrainSuite using the Painter tool
http://brainsuite.org/delineation/roi/label-painter-tool/
If you want to modify the atlas or draw your own ROIs and make your own atlas, you can do that using the custom atlas creation method:
http://brainsuite.org/processing/svreg/creating-custom-atlases/
BrainSuite should be able to process elderly adults.
3. The ROIs are stored as a separate volume in nifti file format. Most brain imaging softwares support nifti format.

[Anand Joshi]

You can run the a command to get color coded brain image of the thickness values
Check module 10 here.
http://brainsuite.org/processing/svreg/svreg_modules/
This script is available in BrainSuite installation directory under svreg subdirectory.
This code is our new thickness measurement method. You can run it from the command line.

• This reply was modified 7 years, 4 months ago by Anand Joshi.

[Anand Joshi]

Please make sure that you have installed matlab MCR 2015b installed.
The later or earlier versions of Matlab MCR do not work. The exact version 2015b is required. The link for the MCR in the installation instructions.
http://brainsuite.org/quickstart/installation/

[Anand Joshi]

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,

[Anand Joshi]

Thank you for running BrainSuite. Here are some instructions for MacOS Sierra. Please make sure that you have followed them. Also make sure that you are running the latest version of BrainSuite.
http://brainsuite.org/2016/11/brainsuite-on-macos-sierra-10-12/

Thanks,

[Anand Joshi]

You should check the outputs in case of this warning. Please check outputs at steps 22 and 23 at the following link:
http://brainsuite.org/tutorials/cseexcercise/
especially check the green curve showing the cerebrum mask.

Please make sure that your outputs look like that. If they do, then you can ignore the warning.

[Anand Joshi]

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.

[Anand Joshi]

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.

[Anand Joshi]

A possible fix it installing 32 bit redistributable from:
https://www.microsoft.com/en-us/download/details.aspx?id=40784
Make sure to install 32bit version of Visual C++ Redistributable Packages for Visual Studio 2013.

[Anand Joshi]

Hi, Thank you for reporting the issue.
Are you able to run the following exe from the command line
> C:\Program Files\BrainSuite16a1\svreg\bin\warp_points.exe

It should show the following message.
> C:\Users\ajoshi>”C:\Program Files\BrainSuite16a1\svreg\bin\warp_points.exe”
>
> Usage: C:\Program Files\BrainSuite16a1\svreg\bin\warp_points.exe .warp_file ucf_in ucf_out

Please let me know what message you get.
Additionally, please make sure that your windows system is up to date with all the updates applied.
Can you please report your windows system configuration?
Thanks,
Anand

• This reply was modified 7 years, 5 months ago by Anand Joshi. Reason: updates
• This reply was modified 7 years, 5 months ago by Anand Joshi.

[Anand Joshi]

I am not able to find your email. What was the subject or email address from which you sent it?

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