{"action":"created","issue":{"url":"https://api.github.com/repos/freesurfer/freesurfer/issues/460","repository_url":"https://api.github.com/repos/freesurfer/freesurfer","labels_url":"https://api.github.com/repos/freesurfer/freesurfer/issues/460/labels{/name}","comments_url":"https://api.github.com/repos/freesurfer/freesurfer/issues/460/comments","events_url":"https://api.github.com/repos/freesurfer/freesurfer/issues/460/events","html_url":"https://github.com/freesurfer/freesurfer/pull/460","id":342740069,"node_id":"MDExOlB1bGxSZXF1ZXN0MjAyNTY4ODQ1","number":460,"title":"WIP: Infant recon for non-MGH users","user":{"login":"larsoner","id":2365790,"node_id":"MDQ6VXNlcjIzNjU3OTA=","avatar_url":"https://avatars1.githubusercontent.com/u/2365790?v=4","gravatar_id":"","url":"https://api.github.com/users/larsoner","html_url":"https://github.com/larsoner","followers_url":"https://api.github.com/users/larsoner/followers","following_url":"https://api.github.com/users/larsoner/following{/other_user}","gists_url":"https://api.github.com/users/larsoner/gists{/gist_id}","starred_url":"https://api.github.com/users/larsoner/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/larsoner/subscriptions","organizations_url":"https://api.github.com/users/larsoner/orgs","repos_url":"https://api.github.com/users/larsoner/repos","events_url":"https://api.github.com/users/larsoner/events{/privacy}","received_events_url":"https://api.github.com/users/larsoner/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2018-07-19T13:58:33Z","updated_at":"2018-07-19T18:03:51Z","closed_at":"2018-07-19T15:16:45Z","author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/freesurfer/freesurfer/pulls/460","html_url":"https://github.com/freesurfer/freesurfer/pull/460","diff_url":"https://github.com/freesurfer/freesurfer/pull/460.diff","patch_url":"https://github.com/freesurfer/freesurfer/pull/460.patch"},"body":"Trying to run the `infant_recon_all`. WIP because I haven't completed a run, but this is to keep track of the changes that were necessary. @lillazollei let me know if this is helpful or not!\r\n\r\n1. Need to add to the Wiki that ~~MATLAB~~ the [MATLAB R2012b Runtime](https://www.mathworks.com/products/compiler/matlab-runtime.html) is required, and the `MATLAB_ROOT` env var needs to be set to point to this.\r\n2. Update wiki that FSL is required.\r\n3. Update wiki that [dramms](https://www.nitrc.org/projects/dramms/) is required.\r\n4. ~~Packaging needs to be fixed to include some or all of `scripts/InfantFS`, or these files need to be moved to `bin` during packaging (if the latter, `InfantFS` instances will need to be replaced in the scripts).~~\r\n5. Use `LabelFusion` from GitHub master rather than the archive.\r\n6. Do not use a relative path for the skull-stripped input or it will break in the `norm.nii.gz` linking step.\r\n\r\nWe'll see if it runs all the way through now."},"comment":{"url":"https://api.github.com/repos/freesurfer/freesurfer/issues/comments/406364658","html_url":"https://github.com/freesurfer/freesurfer/pull/460#issuecomment-406364658","issue_url":"https://api.github.com/repos/freesurfer/freesurfer/issues/460","id":406364658,"node_id":"MDEyOklzc3VlQ29tbWVudDQwNjM2NDY1OA==","user":{"login":"larsoner","id":2365790,"node_id":"MDQ6VXNlcjIzNjU3OTA=","avatar_url":"https://avatars1.githubusercontent.com/u/2365790?v=4","gravatar_id":"","url":"https://api.github.com/users/larsoner","html_url":"https://github.com/larsoner","followers_url":"https://api.github.com/users/larsoner/followers","following_url":"https://api.github.com/users/larsoner/following{/other_user}","gists_url":"https://api.github.com/users/larsoner/gists{/gist_id}","starred_url":"https://api.github.com/users/larsoner/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/larsoner/subscriptions","organizations_url":"https://api.github.com/users/larsoner/orgs","repos_url":"https://api.github.com/users/larsoner/repos","events_url":"https://api.github.com/users/larsoner/events{/privacy}","received_events_url":"https://api.github.com/users/larsoner/received_events","type":"User","site_admin":false},"created_at":"2018-07-19T18:03:51Z","updated_at":"2018-07-19T18:03:51Z","author_association":"CONTRIBUTOR","body":"So far this has fixed the path issues, yeah. I got one subject to run to completion with these changes, which is great! But it didn't do any surface generation because there was no GM/WM boundary (re-running it now to force it to use a template to use for this), so I probably haven't hit complete coverage yet. I'll update if there are other problems :)\r\n\r\nFWIW in the future there are some issues that could be fixed in the scripts themselves, specifically:\r\n\r\n1. `.mgz` is not supported as an as arg to `--masked` (`.nii.gz` at least works, which can be made with `mri_convert`), and\r\n2. passing a relative path to `--masked` rather than an absolute one breaks during a `norm.nii.gz` symbolic linking.\r\n\r\nAnd as I wrote above, the wiki / instructional email probably needs some updates. But these are not show-stoppers."}}
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