{"id":6623,"date":"2023-01-23T12:51:18","date_gmt":"2023-01-23T12:51:18","guid":{"rendered":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=6623"},"modified":"2023-01-23T12:52:17","modified_gmt":"2023-01-23T12:52:17","slug":"dcm2niix","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/tools\/dcm2niix\/","title":{"rendered":"dcm2niix"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"https:\/\/github.com\/rordenlab\/dcm2niix\">dcm2niix<\/a> is a program to convert neuroimaging data from the DICOM format to the NIfTI format.<\/p>\n<p>Version 1.0.20220720 is installed on the CSF. <\/p>\n<h2>Restrictions on use<\/h2>\n<p>There are no restrictions on accessing this software on the CSF. All usage must adhere to the software licenses provided in the <a href=\"https:\/\/github.com\/rordenlab\/dcm2niix\/blob\/master\/license.txt\">license.txt<\/a> file (in the github repo).<\/p>\n<h2>Set up procedure<\/h2>\n<p>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 <abbr title=\"add '#$ -V' to your jobscript\">inherit these settings<\/abbr>.<\/p>\n<p>Load one of the following modulefiles:<\/p>\n<pre>\r\nmodule load apps\/binapps\/dcm2niix\/1.0.20220720\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run dcmi2niix on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<h3>Serial batch job submission<\/h3>\n<p>Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n<pre>\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\nmodule load apps\/binapps\/dcm2niix\/1.0.20220720\r\n\r\ndcm2niix <em>args ...<\/em>\r\n  #\r\n  # Alternatively the dcmi2niibatch executable is also available\r\n<\/pre>\n<p>Submit the jobscript using: <\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"https:\/\/www.nitrc.org\/plugins\/mwiki\/index.php\/dcm2nii:MainPage\">dcm2niix manual<\/a><\/li>\n<li><a href=\"https:\/\/github.com\/rordenlab\/dcm2niix\">dcm2niix manual<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview dcm2niix is a program to convert neuroimaging data from the DICOM format to the NIfTI format. Version 1.0.20220720 is installed on the CSF. Restrictions on use There are no restrictions on accessing this software on the CSF. All usage must adhere to the software licenses provided in the license.txt file (in the github repo). Set up procedure We now recommend loading modulefiles within your jobscript so that you have a full record of how.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/tools\/dcm2niix\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":144,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-6623","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/6623","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=6623"}],"version-history":[{"count":1,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/6623\/revisions"}],"predecessor-version":[{"id":6624,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/6623\/revisions\/6624"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/144"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=6623"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}