[shjoshi]

Thanks. I recon this is due to the file separators on Windows.
Can you please do the following?

1. Can you run
check_file_exists(“D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/2011101206/2011101206.svreg.log”)

2. Attach/paste the contents of the file 2011101206.svreg.log

3. Run get_brainsuite_install_path()

4. get_brainsuite_atlas_id_from_logfile(“D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/2011101206/2011101206.svreg.log”)

[shjoshi]

Hmm. Can you do one more thing?
Type these 3 commands:

file.path(‘D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/’, “2011101206”, ‘*.svreg.log’)

Sys.glob(file.path(‘D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/’, “2011101206”, ‘*.svreg.log’))

check_file_exists(Sys.glob(file.path(‘D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/’, “2011101206”, ‘*.svreg.log’)))

[shjoshi]

Hi Tetsuya,

Does the path D:/Tetsuya/All_data/MRI/DTIandMPRAGE/38NC/2011101206 actually exist on disk?

I.e. Does the directory DTIandMPRAGE exist in the directory MRI?
Or did you just change & to and in the command?

Thanks,
Shantanu

[shjoshi]

Hm.. Is this because of the “&” in the file name?
In RStudio, what does
dir(“D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/2011101206/2011101206.svreg.log”)
give you?

Please not the quotes “” above may not be correctly formatted online. Please don’t copy the command as is, but type in the start and the end quotes.

• This reply was modified 6 years, 7 months ago by shjoshi.
• This reply was modified 6 years, 7 months ago by shjoshi.

[shjoshi]

Hm.. Is this because of the “&” in the file name?
In RStudio, what does
dir(‘D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/2011101206/2011101206.svreg.log’)
give you?

[shjoshi]

Hi Tetsuya,

A couple of things…
1. Is the “&” in your path creating this problem?
2. Does your path start with D, or is this D:/ ?

Also you could run the stats on the command line, but I would suggest running it through RStudio. It’s easier and you can do this step by step.

I’ve added tutorial slides in the bottom at http://brainsuite.org/bssr/ for standard usage cases.

Shantanu

[shjoshi]

Glad to know the installation worked out.

[shjoshi]

Hi Tetsuya,

We have now ported BSS to R. You can find the link at http://brainsuite.org/bssr
The instructions to install are much simpler and should work for you on Windows.
Can you please give it a try?

Thanks,
Shantanu

[shjoshi]

If bss is installed in /usr/local/lib/python2.7, then bss_prepare_data_for_tbm.py should go in the bin directory where you are calling python from. For e.g.
/usr/local/bin, /usr/bin etc..

you can do
which pip
or
which python

bss_prepare_data_for_tbm.py should be in the bin directory where your pip or python is located.

S

[shjoshi]

Hi Alice,

If you installed bss using pip install bss, then I’m suspecting it must be installed in /usr/local/lib/python2.7/site-packages/bss or some such location.

Did you move the bss folder to /Applications by any chance?

I noticed you typed /Application/
In the command you actually ran, I’m assuming you typed /Applications/ since that’s the correct folder name on Mac.

Thanks,
Shantanu

PS: I should also let you know, that we are moving bss from python to R in the future. The release will happen before the end of this month. So if you were not in a rush to analyze the data, you could wait for the r package release. Just a thought.

[shjoshi]

Hello,

It seems even if you invoked install.sh with sudo, some of the installation files were not written to /usr/share.

Can you actually try installing bss in your user or home directory, where you don’t need sudo?

[shjoshi]

Hmm. is it possible to paste the entire error including the output on the screen when you run the installation command?

Thanks,
Shantanu

[shjoshi]

Yes, we are trying to work on it. Some packages cannot be compiled from source on Windows very easily so we need to make the binaries available. This makes the installation process complicated.

We are hoping that with the release of the new bash shell in Windows 10, the installation process may become easier.

Thanks,
Shantanu

[shjoshi]

Hi Alexander,

I was wondering if you can repost this message in the SVREG forum (https://forums.brainsuite.org/forums/forum/svreg/)

This is directly seen by the svreg developers who will be able to answer your question.

Thanks,
Shantanu

[shjoshi]

Hi Dr. Neyaz,

We have now made the installation process on Linux/Mac much simpler.
The new instructions are located at
http://brainsuite.org/bss/bss-download/

Essentially you just have to download the install.sh script and run it as:

bash install.sh <full path to the bss installation directory>

The above problem will have been fixed in this version.

Thanks,
Shantanu

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