For my project, I am working on DWI data of 150 subjects and obtained connectivity matrices base on fa and adc in the pickle format . The matrix size is 124X124 and to avoid wasting time I need to obtain graph features such as small worldness and centrality using command line for all subjects.
I have worked with gretna, brain connectivity toolbox and BRAPH but as you know these toolboxes work with GUI and it takes a long time to run them for all subjects.
Thanks in advance to your attentions or maybe your helps
Dear Colleague,
Brain Connectivity Toolbox (https://sites.google.com/site/bctnet/?pli=1) is actually what you are looking for. It works through "command line", as you request, has all the functionalities that you need, and most importantly is up-to-date.
Best,
Simone
Dear Dr Di Plinio
Many thanks for your answer and sharing the link. I have worked with this toolbox using its GUI but not command line or scripting. Do you have any tutorial ((detailed video, booklet etc.) for running the toolbox using command line?
Best regards,
-Milad
Dear Milad,
There is a new version of BRAPH (BRAPH2) out at http://braph.org, which can be used via its GUI and it is scriptable as well. There are extensive tutorials on how to do both at the website.
Best,
Daniel
Dear Milad,
Medusa-kernel (https://github.com/medusabci/medusa-kernel) is a modern Python toolbox intended for both brain-computer interface design and evaluation and signal analysis. It includes functional connectivity methods and an extensive package with graph theory methods such as node strength, small world, betweenness centrality.... I think it could be useful in your project.
Here is the documentation: https://docs.medusabci.com/kernel/1.1.3/documentation.php
I hope you find it interesting.
Best regards,
Diego
Dear Dr Vereb and Dr Martinez
Many thanks. Regarding the BRAPH2, I try to work it using script and sharing my results. I also tried to install Medusa-kernel but there was an error during installation using pip as follow:
pip install medusa-kernel
Collecting medusa-kernel
Using cached medusa_kernel-1.1.3-py3-none-any.whl (260 kB)
Collecting bson
Downloading dill-0.3.6-py3-none-any.whl (110 kB)
|██████████████████████████▊ | 92 kB 25 kB/s eta 0:00:01ERROR: Exception:
Traceback (most recent call last):
File "/usr/share/python-wheels/urllib3-1.25.8-py2.py3-none-any.whl/urllib3/response.py", line 425, in _error_catcher
yield
File "/usr/share/python-wheels/urllib3-1.25.8-py2.py3-none-any.whl/urllib3/response.py", line 507, in read
data = self._fp.read(amt) if not fp_closed else b""
File "/usr/share/python-wheels/CacheControl-0.12.6-py2.py3-none-any.whl/cachecontrol/filewrapper.py", line 62, in read
data = self.__fp.read(amt)
File "/usr/lib/python3.8/http/client.py", line 459, in read
n = self.readinto(b)
File "/usr/lib/python3.8/http/client.py", line 503, in readinto
n = self.fp.readinto(b)
File "/usr/lib/python3.8/socket.py", line 669, in readinto
return self._sock.recv_into(b)
File "/usr/lib/python3.8/ssl.py", line 1241, in recv_into
return self.read(nbytes, buffer)
File "/usr/lib/python3.8/ssl.py", line 1099, in read
return self._sslobj.read(len, buffer)
socket.timeout: The read operation timed out
How can i solve it?
Best Regards,
Milad
Dear Milad Najafzadeh
You seem to have had some problem with your internet connection (see "socket.timeout: The read operation timed out" error). I recommend you to download and install a 3.9 64bit version of Python and try to install medusa-kernel in your virtual environment again. If you still have problems, don't hesitate to write me!
Best,
Diego.
Dear Milad Najafzadeh
The NetworkX is an open-source Python package for network analysis receiving the adjacency matrixes for network analysis. You can, consequently, calculate a wide range of network properties
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