{"action":"created","issue":{"url":"https://api.github.com/repos/poldracklab/fmriprep/issues/1001","repository_url":"https://api.github.com/repos/poldracklab/fmriprep","labels_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/1001/labels{/name}","comments_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/1001/comments","events_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/1001/events","html_url":"https://github.com/poldracklab/fmriprep/pull/1001","id":299068629,"number":1001,"title":"ENH: generate CIFTI derivatives","user":{"login":"mgxd","id":14110164,"avatar_url":"https://avatars1.githubusercontent.com/u/14110164?v=4","gravatar_id":"","url":"https://api.github.com/users/mgxd","html_url":"https://github.com/mgxd","followers_url":"https://api.github.com/users/mgxd/followers","following_url":"https://api.github.com/users/mgxd/following{/other_user}","gists_url":"https://api.github.com/users/mgxd/gists{/gist_id}","starred_url":"https://api.github.com/users/mgxd/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mgxd/subscriptions","organizations_url":"https://api.github.com/users/mgxd/orgs","repos_url":"https://api.github.com/users/mgxd/repos","events_url":"https://api.github.com/users/mgxd/events{/privacy}","received_events_url":"https://api.github.com/users/mgxd/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":25,"created_at":"2018-02-21T17:56:52Z","updated_at":"2018-04-05T16:09:07Z","closed_at":null,"author_association":"COLLABORATOR","pull_request":{"url":"https://api.github.com/repos/poldracklab/fmriprep/pulls/1001","html_url":"https://github.com/poldracklab/fmriprep/pull/1001","diff_url":"https://github.com/poldracklab/fmriprep/pull/1001.diff","patch_url":"https://github.com/poldracklab/fmriprep/pull/1001.patch"},"body":"ref. #794 \r\n\r\n* converts bold/gii data to CIFTI dtseries file\r\n  * `fsaverage5`/`fsaverage6` surfaces + `MNI2009NLin2009cAsym` subcortical volumes\r\n* adds `compress` input to `DerivativesDataSink`\r\n* increases required niworkflows to 0.3.5\r\n\r\n###### TODOs\r\n* [x] complete interface\r\n* [x] add to bold workflow\r\n* [x] add testing\r\n\r\n###### To be added in another PR\r\n* create HCP 91282 greyordinate space CIFTIs (#1025)\r\n* support `fsnative` surface + subject space `aparc+aseg`\r\n  * number of indices in fsaverage5 (~10k) vs fsnative (+100k) will make these files fairly large\r\n"},"comment":{"url":"https://api.github.com/repos/poldracklab/fmriprep/issues/comments/378989899","html_url":"https://github.com/poldracklab/fmriprep/pull/1001#issuecomment-378989899","issue_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/1001","id":378989899,"user":{"login":"mgxd","id":14110164,"avatar_url":"https://avatars1.githubusercontent.com/u/14110164?v=4","gravatar_id":"","url":"https://api.github.com/users/mgxd","html_url":"https://github.com/mgxd","followers_url":"https://api.github.com/users/mgxd/followers","following_url":"https://api.github.com/users/mgxd/following{/other_user}","gists_url":"https://api.github.com/users/mgxd/gists{/gist_id}","starred_url":"https://api.github.com/users/mgxd/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mgxd/subscriptions","organizations_url":"https://api.github.com/users/mgxd/orgs","repos_url":"https://api.github.com/users/mgxd/repos","events_url":"https://api.github.com/users/mgxd/events{/privacy}","received_events_url":"https://api.github.com/users/mgxd/received_events","type":"User","site_admin":false},"created_at":"2018-04-05T16:09:07Z","updated_at":"2018-04-05T16:09:07Z","author_association":"COLLABORATOR","body":"I'm trying to build a docker container off this branch, but am running into a peculiar error.\r\n\r\n#### First attempt - build a new docker image from my repo.\r\n```\r\ndocker build -t cifti-fmriprep .\r\n```\r\nOnce successfully built, I tried running a subject, but was given this error:\r\n```\r\n180405-15:54:42,857 workflow IMPORTANT:\r\n\t \r\n    Running fMRIPREP version :\r\n      * BIDS dataset path: /data.\r\n      * Participant list: ['BANDA001'].\r\n      * Run identifier: 20180405-155442_f08b40e4-9a37-425a-9c3e-d1ec8ef8c21d.\r\n    \r\n/usr/local/miniconda/lib/python3.6/site-packages/grabbit/core.py:410: UserWarning: No valid root directory found for domain 'derivatives'. Falling back on the Layout's root directory. If this isn't the intended behavior, make sure the config file for this domain includes a 'root' key.\r\n  \"'root' key.\" % config['name'])\r\n180405-15:54:43,853 workflow IMPORTANT:\r\n\t Creating bold processing workflow for \"/data/sub-BANDA001/func/sub-BANDA001_task-conflict_run-01_bold.nii.gz\" (0.32 GB / 280 TRs). Memory resampled/largemem=1.28/2.17 GB.\r\nProcess Process-2:\r\nTraceback (most recent call last):\r\n  File \"/usr/local/miniconda/lib/python3.6/multiprocessing/process.py\", line 249, in _bootstrap\r\n    self.run()\r\n  File \"/usr/local/miniconda/lib/python3.6/multiprocessing/process.py\", line 93, in run\r\n    self._target(*self._args, **self._kwargs)\r\n  File \"/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py\", line 451, in build_workflow\r\n    ignore_aroma_err=opts.ignore_aroma_denoising_errors,\r\n  File \"/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py\", line 199, in init_fmriprep_wf\r\n    ignore_aroma_err=ignore_aroma_err)\r\n  File \"/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py\", line 450, in init_single_subject_wf\r\n    ignore_aroma_err=ignore_aroma_err)\r\n  File \"/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/bold/base.py\", line 397, in init_func_preproc_wf\r\n    bold_sdc_wf.inputs.inputnode.template = template\r\nAttributeError: 'TraitedSpec' object has no attribute 'inputnode'\r\n```\r\n\r\nHowever, using the `poldracklab/fmriprep:latest` image did not result in the error.\r\n\r\n#### Second attempt - bind cifti fmriprep fork within `poldracklab/fmriprep:latest`\r\n\r\n```\r\ndocker run --rm -it -v /code/datasets/banda:/data \\\r\n-v /code/fmriprep/fmriprep:/usr/local/miniconda/lib/python3.6/site-packages/fmriprep:ro \\\r\n-v /home/mathias/code/workdir/niworkflows/niworkflows/data:/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/data:ro poldracklab/fmriprep:latest \\\r\n/data /data/derivatives participant --participant_label BANDA001 \\\r\n--fs-license-file /data/code/.freesurfer_license.txt --ignore slicetiming\r\n```\r\n\r\nThis results in the same error (but now version is shown as `0+unknown`)\r\n\r\n```\r\n180405-16:05:14,264 workflow IMPORTANT:\r\n\t \r\n    Running fMRIPREP version 0+unknown:\r\n      * BIDS dataset path: /data.\r\n      * Participant list: ['BANDA001'].\r\n      * Run identifier: 20180405-160514_2ebd676a-c387-445a-b20c-9100a66eb9f0.\r\n    \r\n/usr/local/miniconda/lib/python3.6/site-packages/grabbit/core.py:410: UserWarning: No valid root directory found for domain 'derivatives'. Falling back on the Layout's root directory. If this isn't the intended behavior, make sure the config file for this domain includes a 'root' key.\r\n  \"'root' key.\" % config['name'])\r\n180405-16:05:15,307 workflow IMPORTANT:\r\n\t Creating bold processing workflow for \"/data/sub-BANDA001/func/sub-BANDA001_task-conflict_run-01_bold.nii.gz\" (0.32 GB / 280 TRs). Memory resampled/largemem=1.28/2.17 GB.\r\nProcess Process-2:\r\nTraceback (most recent call last):\r\n  File \"/usr/local/miniconda/lib/python3.6/multiprocessing/process.py\", line 249, in _bootstrap\r\n    self.run()\r\n  File \"/usr/local/miniconda/lib/python3.6/multiprocessing/process.py\", line 93, in run\r\n    self._target(*self._args, **self._kwargs)\r\n  File \"/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py\", line 451, in build_workflow\r\n    ignore_aroma_err=opts.ignore_aroma_denoising_errors,\r\n  File \"/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py\", line 199, in init_fmriprep_wf\r\n    ignore_aroma_err=ignore_aroma_err)\r\n  File \"/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py\", line 450, in init_single_subject_wf\r\n    ignore_aroma_err=ignore_aroma_err)\r\n  File \"/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/bold/base.py\", line 397, in init_func_preproc_wf\r\n    bold_sdc_wf.inputs.inputnode.template = template\r\nAttributeError: 'TraitedSpec' object has no attribute 'inputnode'\r\n```\r\n\r\n#### Third attempt - binding my fork of master within `poldracklab/fmriprep:latest`\r\n\r\nAgain, the same error - I'm not sure why this is happening...\r\n\r\nHowever, all tests pass on the CI, so this leads me to believe it's something with my machine.\r\n\r\n@oesteban any chance you could give this another (final?) review"}}
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