{"id":7442,"date":"2024-02-20T19:04:59","date_gmt":"2024-02-20T19:04:59","guid":{"rendered":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=7442"},"modified":"2024-02-20T19:19:11","modified_gmt":"2024-02-20T19:19:11","slug":"sclimbic","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/sclimbic\/","title":{"rendered":"ScLimbic"},"content":{"rendered":"

Overview<\/h2>\n

ScLimbic<\/a> provides a deep learning tool, mri_sclimbic_seg<\/code>, to automatically segment several subcorical limbic structures from T1-weighted images (“SC” = subcortical). The structures are shown in the figure below (note: anterior commissure is only present for reference reasons).<\/p>\n

Version 2021-07-25 is installed on the CSF.<\/p>\n

Restrictions on use<\/h2>\n

We have restricted access to this application to only those people with access to FreeSurfer. Hence you should read the Restrictions on Use<\/a> section of the FreeSurfer page and follow the instructions there to request access to FreeSurfer. You will not be able to run ScLimbic if you do not yet have access to FreeSurfer.<\/strong><\/p>\n

The authors of this software also state that those using this toolbox should cite: “A Deep Learning Toolbox for Automatic Segmentation of Subcortical Limbic Structures from MRI Images. Greve, DN, Billot, B, Cordero, D, Hoopes, A, Hoffmann, M, Dalca, A, Fischl, B, Iglesias, JE, Augustinack, JC. Accepted. Neuroimage 2021. 10.1016\/j.neuroimage.2021.118610. PMID: 34571161.” https:\/\/pubmed.ncbi.nlm.nih.gov\/34571161<\/a>. PDF Available here<\/a>.<\/p>\n

Set up procedure<\/h2>\n

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings<\/abbr>.<\/p>\n

Load one of the following modulefiles:<\/p>\n

\r\n# Please note: you must not<\/em> have any freesurfer modulefiles loaded to use this modulefile!\r\nmodule load apps\/binapps\/sclimbic\/20210725\r\n<\/pre>\n
Running the application<\/h2>\n
Please do not run mri_sclimbic_seg<\/code> or freeview<\/code> on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n
You may run mri_sclimbic_seg --help<\/code> to see a list of command-line flags that you may wish to use when writing your jobscripts.<\/p>\n
Running ScLimbic and FreeSurfer<\/h3>\n
It is not possible to load both a freesurfer<\/code> modulefile and a sclimbic<\/code> modulefile. <\/p>\n
If you wish to run both apps in the same jobscript, you should load one, run the app, then unload that modulefile and load the next. For example<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -cwd\r\n\r\n# This will set SUBJECTS_DIR to ~\/scratch\/subjects\r\nmodule load apps\/binapps\/freesurfer\/7.4.1\r\nfreesurfer commands<\/em>\r\n\r\n# Unload all modulefiles\r\nmodule purge\r\n\r\n# Note that this will also set SUBJECTS_DIR to ~\/scratch\/subjects if you've not already set it\r\nmodule load apps\/binapps\/sclimbic\/20210725\r\nsclimibic commands<\/em>\r\n            #\r\n            # See below for a basic command-line\r\n<\/pre>\n
Sample Volume<\/h3>\n
The installation comes with the bert.t1.mgz<\/code> sample volume, which can be found at $SCLIMBICDIR\/bert.t1.mgz<\/code> after loading the modulefile.<\/p>\n
Serial batch job submission<\/h3>\n
Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n
\r\n#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\n                    # NO -V line - we load modulefiles in the jobscript\r\n\r\n# Please note, you CANNOT have any freesurfer modulefiles loaded at this point.\r\nmodule load apps\/binapps\/sclimbic\/20210725\r\n\r\nmri_sclimbic_seg --i input_vol<\/em>.mgz --o output_vol<\/em>.mgz\r\n  #\r\n  # See the ScLimbic website for more command-lines\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Parallel batch job submission<\/h3>\n
Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n
\r\n#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -pe smp.pe 4     # Number of cores (2--32)\r\n                    # NO -V line - we load modulefiles in the jobscript\r\n\r\n# Please note, you CANNOT have any freesurfer modulefiles loaded at this point.\r\nmodule load apps\/binapps\/sclimbic\/20210725\r\n\r\nmri_sclimbic_seg --threads $NSLOTS --i input_vol<\/em>.mgz --o output_vol<\/em>.mgz\r\n  #\r\n  # See the ScLimbic website for more command-lines                                        #\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Using the freeview viewer<\/h2>\n
This should be run in an interactive session, which will run the app on a compute node but display it on your laptop\/PC as follows:<\/p>\n
\r\n# On the CSF login node:\r\nmodule load apps\/binapps\/sclimbic\/20210725\r\ncd ~\/scratch\/where\/your\/volumes\/are\r\nqrsh -l short -cwd -V freeview vol.mgz\r\n<\/pre>\n
Further info<\/h2>\n