{"id":629,"date":"2023-03-30T10:00:01","date_gmt":"2023-03-30T14:00:01","guid":{"rendered":"https:\/\/psycomp.utsc.utoronto.ca\/support\/?p=629"},"modified":"2023-04-10T04:11:07","modified_gmt":"2023-04-10T08:11:07","slug":"use-fmriprep-on-cluster","status":"publish","type":"post","link":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/2023\/03\/30\/use-fmriprep-on-cluster\/","title":{"rendered":"Use fMRIPrep on Cluster"},"content":{"rendered":"<p>\r\n<strong>After you connect to the head node, you can start a Slurm session using the following command, for example:<\/strong>\r\n<pre>\r\nsrun -c 12 --x11 --pty bash -i\r\n<\/pre>\r\n<strong>Then run the following commands to set up the environment:<\/strong>\r\n<pre>\r\nmodule load nodejs\r\nmodule load afni\r\nmodule load ants\r\nmodule load c3d\r\nmodule load connectome-workbench\r\nsource \/opt\/scripts\/user\/conda3-2020.11.init.sh\r\nconda activate fmriprep\r\n<\/pre>\r\nThe first time you run the above &#8220;module load afni&#8221; command, it will configure <a href=\"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/2021\/01\/18\/run-afni-on-cluster\/\" target=\"_blank\" rel=\"noopener\">AFNI<\/a> for you and copy the default data to your home folder. Configuration and data copying won&#8217;t happen again unless your &#8220;~\/.afnirc&#8221; file is deleted or modified, or a newer version of AFNI is available on the cluster.<br\/><br\/>\r\n<strong>You can then run &#8220;fmriprep&#8221; command, for example, to check the vesion:<\/strong>\r\n<pre>\r\nfmriprep --version\r\n<\/pre>\r\n<p><strong>The current fMRIPrep version is fMRIPrep v23.0.1 (Jan 14, 2021).<\/strong><\/p>\r\n","protected":false},"excerpt":{"rendered":"<p>After you connect to the head node, you can start a Slurm session using the following command, for example: srun -c 12 &#8211;x11 &#8211;pty bash -i Then run the following commands to set up the environment: module load nodejs module &hellip;<\/p>\n<p class=\"read-more\"> <a class=\"\" href=\"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/2023\/03\/30\/use-fmriprep-on-cluster\/\"> <span class=\"screen-reader-text\">Use fMRIPrep on Cluster<\/span> Read More &raquo;<\/a><\/p>\n","protected":false},"author":5,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"categories":[3,7,5,10,4],"tags":[],"class_list":["post-629","post","type-post","status-publish","format-standard","hentry","category-clusterinfo","category-linuxshell","category-python","category-slurm","category-software"],"_links":{"self":[{"href":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/wp-json\/wp\/v2\/posts\/629","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/wp-json\/wp\/v2\/users\/5"}],"replies":[{"embeddable":true,"href":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/wp-json\/wp\/v2\/comments?post=629"}],"version-history":[{"count":4,"href":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/wp-json\/wp\/v2\/posts\/629\/revisions"}],"predecessor-version":[{"id":633,"href":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/wp-json\/wp\/v2\/posts\/629\/revisions\/633"}],"wp:attachment":[{"href":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/wp-json\/wp\/v2\/media?parent=629"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/wp-json\/wp\/v2\/categories?post=629"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/wp-json\/wp\/v2\/tags?post=629"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}