{"action":"created","issue":{"url":"https://api.github.com/repos/nipy/nipype/issues/1326","repository_url":"https://api.github.com/repos/nipy/nipype","labels_url":"https://api.github.com/repos/nipy/nipype/issues/1326/labels{/name}","comments_url":"https://api.github.com/repos/nipy/nipype/issues/1326/comments","events_url":"https://api.github.com/repos/nipy/nipype/issues/1326/events","html_url":"https://github.com/nipy/nipype/pull/1326","id":127944104,"number":1326,"title":"ENH: FreeSurfer Wrappings for Recon-All Workflow","user":{"login":"dgellis90","id":8558995,"avatar_url":"https://avatars.githubusercontent.com/u/8558995?v=3","gravatar_id":"","url":"https://api.github.com/users/dgellis90","html_url":"https://github.com/dgellis90","followers_url":"https://api.github.com/users/dgellis90/followers","following_url":"https://api.github.com/users/dgellis90/following{/other_user}","gists_url":"https://api.github.com/users/dgellis90/gists{/gist_id}","starred_url":"https://api.github.com/users/dgellis90/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dgellis90/subscriptions","organizations_url":"https://api.github.com/users/dgellis90/orgs","repos_url":"https://api.github.com/users/dgellis90/repos","events_url":"https://api.github.com/users/dgellis90/events{/privacy}","received_events_url":"https://api.github.com/users/dgellis90/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2016-01-21T15:03:55Z","updated_at":"2016-02-06T14:51:01Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/nipy/nipype/pulls/1326","html_url":"https://github.com/nipy/nipype/pull/1326","diff_url":"https://github.com/nipy/nipype/pull/1326.diff","patch_url":"https://github.com/nipy/nipype/pull/1326.patch"},"body":"This pull request add the wrappings for the following FreeSurfer commands:\r\n* mri_nu_correct.mni\r\n* mri_watershed\r\n* mri_normalize\r\n* mri_ca_normalize\r\n* mri_ca_register\r\n* mri_ca_label\r\n* mris_ca_label\r\n* mri_cc\r\n* mri_segment\r\n* mri_edit_wm_with_aseg\r\n* mri_concatenate_lta\r\n* mri_label2label\r\n* mris_label2annot\r\n* mris_spherical_average\r\n* mri_add_xform_to_header\r\n* talairach_afd\r\n* talairach_avi\r\n* tal_QC_AZS\r\n* mri_remove_neck\r\n* mri_fill\r\n* mris_inflate\r\n* mris_sphere\r\n* mris_fix_topology\r\n* mris_euler_number\r\n* mris_remove_intersection\r\n* mris_make_surfaces\r\n* mris_curvature\r\n* mris_curvature_stats\r\n* mris_jacobian\r\n* mris_calc\r\n* mris_volmask\r\n* mris_anatomical_stats\r\n* pctsurfcon\r\n* mri_relabel_hypointensities\r\n* mri_aparc2aseg\r\n* apas2aseg\r\n* mri_robust_template\r\n* mri_fuse_segmentations\r\n* mpr2mni305\r\n* avi2talxfm\r\n* mri_em_register\r\n* mris_register\r\n* mrisp_paint\r\n\r\n\r\nThis pull requests also adds inputs to some of the existing wrappings for FreeSurfer commands. These wrappings and changes were needed to create a a recon-all workflow in nipype that performs the same steps as recon-all. The workflows and usage information can be found here:\r\nhttps://github.com/BRAINSia/BRAINSTools/tree/FreeSurferBreakout/AutoWorkup/fs_nipype"},"comment":{"url":"https://api.github.com/repos/nipy/nipype/issues/comments/180781344","html_url":"https://github.com/nipy/nipype/pull/1326#issuecomment-180781344","issue_url":"https://api.github.com/repos/nipy/nipype/issues/1326","id":180781344,"user":{"login":"satra","id":184063,"avatar_url":"https://avatars.githubusercontent.com/u/184063?v=3","gravatar_id":"","url":"https://api.github.com/users/satra","html_url":"https://github.com/satra","followers_url":"https://api.github.com/users/satra/followers","following_url":"https://api.github.com/users/satra/following{/other_user}","gists_url":"https://api.github.com/users/satra/gists{/gist_id}","starred_url":"https://api.github.com/users/satra/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/satra/subscriptions","organizations_url":"https://api.github.com/users/satra/orgs","repos_url":"https://api.github.com/users/satra/repos","events_url":"https://api.github.com/users/satra/events{/privacy}","received_events_url":"https://api.github.com/users/satra/received_events","type":"User","site_admin":false},"created_at":"2016-02-06T14:51:01Z","updated_at":"2016-02-06T14:51:01Z","body":"@hjmjohnson - as soon as i saw this i was so excited i wrote to the freesurfer folks to get hold of their testing data. i will let you guys know when i see their test suite.\r\n\r\nis there a place where you have testing results from running this and comparing different stages?"}}