I have had a look at nipype but it does not have the longitudinal processing available yet. I was wondering if there was another way to do this on the RAP? My access level is such that I cannot download any of the imaging files to process it locally.
Freesurfer, FSL and Nipype are part of the JupyterLab IMAGE_PROCESSING flavor. You can just launch Jupyter or work with Docker and do all your planned work on RAP.
There are some training materials and demo for how researcher would use the UKB RAP for image analysis:
Hi Ondrej,
Sorry for the stupid questions but I am having difficulty in setting the directory (SUBJECTS_DIR) in the Terminal. I have my data in the ?working? instance and so have set SUBJECTS_DIR as a folder in the ?working instance? rather than DNAnexus. However it keeps telling me that the directory does not exist when I try to run recon-all. Can you please advise?
Thanks in advance for any guidance you can give me.
Cheryl
Comments
6 comments
Freesurfer, FSL and Nipype are part of the JupyterLab IMAGE_PROCESSING flavor. You can just launch Jupyter or work with Docker and do all your planned work on RAP.
There are some training materials and demo for how researcher would use the UKB RAP for image analysis:
https://github.com/dnanexus/OpenBio/tree/master/image_processing
https://www.youtube.com/watch?v=d6uEl4U8NEM&list=PLRkZ0Fz-n3Z7Jg0Vz4vudLYnBza4EUGLM&index=11
https://www.youtube.com/watch?v=BMAgenSxF_o&list=PLRkZ0Fz-n3Z7Jg0Vz4vudLYnBza4EUGLM&index=2
Anyway, this is a really interesting topic, looking forward to discuss more.
Hi Ondrej,
Thank you for your response! I have watched the Webinar but I'm afraid I'm still stuck.
Is there a way to run FreeSurfer in JupyterLab IMAGE_PROCESSING without using Nipype? Nipype does not support FreeSurfer's longitudinal preprocessing as of yet (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing).
I haven't used Docker before so was hoping there would be an alternative before I try to figure that out!
Thanks,
Cheryl
No need to use Nipype in order get Freesurfer commands. You can access Freesurfer from the JupyterLab Terminal:
If you would like to know more about Docker on RAP:
https://community.dnanexus.com/s/question/0D5t000004412dYCAQ/material-for-the-reproducible-research-using-docker-webinar
Ah great! I'll give it a go. Thank you!
In the JupyterLab, default "working" directory is /opt/notebooks/, so I think you can find your downloaded data there.
An unrelated note, I am seeing that SUBJECTS_DIR is also a predefined variable for Freesurfer, so you can try to move your data to the folder:
You could also test directly specifying inputs such as:
recon-all -i </opt/notebooks/invol_1> -subjid subject_name
I also think that you will need to activate a Freesurfer license (which is free) and point Freesurfer to it . Let's give it a try and will see.
https://surfer.nmr.mgh.harvard.edu/fswiki/License
Please sign in to leave a comment.