Installation and setup

[mmsarhan]

I am having trouble installing all the prerequisite programs before installing pydesigner. I was able to install acaconda and create a python environment with python 3.7. The issue I keep running into is that FSL will not download properly. It will get to the post installation set and fail. I am not sure if I am setting my program wrong or if it is something else. Hopefully someone can help. Thank you.

[TheJaeger]

Hey @mmsarhan, could you post the error from your FSL installation? It would also be helpful if you post your OS and machine information.

[mmsarhan]

Hello @TheJaeger
Below is the message that I received. I am using a VM with Centos 7.

Stage 1
By installing this python distribution you agree to the license terms in
/usr/local/fsl/fslpython/LICENSE.txt
100%
Stage 2
100%
Post install setup failed
[OK] Post installation setup complete
Setting up FSL software...
[OK] User profile updated with FSL settings, you will need to log out and back in to use the FSL tools.
To use FSLView please install the PNG12 and MNG libraries with: sudo yum install libpng12 libmng

[TheJaeger]

I believe it should be fine even if post-install scripts fail, you can repeat those steps manually. The most important tasks this post-install script does are configure FSL variables and PATH. You can do this manually on CentOS by adding the following lines to /etc/profile.d:

FSLDIR=/usr/local/fsl
FSLOUTPUTTYPE=NIFTI_GZ
PATH=$PATH:$FSLDIR/bin
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$FSLDIR

Then logout and login to your VM. FSL commands should then work.

EDIT: Alternatively, you may pull a pre-built Docker container containing FSL, MRtrix3, and PyDesigner called NeuroDock. You can also download the PyDesigner repo/release, cd into the PyDesigner/docker, and build the image manually with

docker build -t dmri/neurodock:v1.0-RC11 -f Dockerfile-release .

If you prefer Singularity over Docker, you may build the same file with Singularity instead.

[mmsarhan]

Where would I find /etc/profile.d: Also are those command all one command or each a different command I have to run? Mutaz M. Sarhan, MS, BS Research Specialist II Laboratory for Precision Brain Imaging Department of Neuroscience Medical University of South Carolina From: Siddhartha Dhiman ***@***.***> Date: Wednesday, December 1, 2021 at 2:54 PM To: m-ama/PyDesigner ***@***.***> Cc: Sarhan, Mutaz ***@***.***>, Mention ***@***.***> Subject: Re: [m-ama/PyDesigner] Installation and setup (Discussion #271) CAUTION: External I believe it should be fine even if post-install scripts fail, you can repeat those steps manually. The most important tasks this post-install script does are configure FSL variables and PATH. You can do this manually on CentOS by adding the following lines to /etc/profile.d: FSLDIR=/usr/local/fsl FSLOUTPUTTYPE=NIFTI_GZ PATH=$PATH:$FSLDIR/bin LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$FSLDIR Then logout and login to your VM. FSL commands should then work. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https:/github.com/m-ama/PyDesigner/discussions/271*discussioncomment-1731155__;Iw!!Ab1_Rw!RvYS8gt8uWwHhnaQkXarBH4P4SRWXxFKG2wo6mKsog2dNFbpRgEja0dyqCBGjg$>, or unsubscribe<https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AWXURMQI3HZYSO57GM6XTR3UOZ4NTANCNFSM5JFBMWCQ__;!!Ab1_Rw!RvYS8gt8uWwHhnaQkXarBH4P4SRWXxFKG2wo6mKsog2dNFbpRgEja0eFozSAGg$>. Triage notifications on the go with GitHub Mobile for iOS<https://urldefense.com/v3/__https:/apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675__;!!Ab1_Rw!RvYS8gt8uWwHhnaQkXarBH4P4SRWXxFKG2wo6mKsog2dNFbpRgEja0exo0XEQw$> or Android<https://urldefense.com/v3/__https:/play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign*3Dnotification-email*26utm_medium*3Demail*26utm_source*3Dgithub__;JSUlJSU!!Ab1_Rw!RvYS8gt8uWwHhnaQkXarBH4P4SRWXxFKG2wo6mKsog2dNFbpRgEja0dxLX3jBg$>.

[TheJaeger]

Please see issue #242 for a fix.

[mmsarhan]

@TheJaeger
pydesigner installed successful. How do I make sure everythin is running correctly?

[TheJaeger]

You can run the command pydesigner --version. It should output the version if FSL, MRtrix, and PyDesigner are installed correctly.

[mmsarhan]

I jut ran the command and it gave me this version so Im assuming everything should be downloaded correctly?
(DKE) [blab@localhost PyDesigner-master]$ pydesigner --version
v1.0-RC11

[TheJaeger]

There you go, it's ready for processing.