{"action":"created","comment":{"url":"https://api.github.com/repos/nipy/nipype/pulls/comments/36040691","id":36040691,"diff_hunk":"@@ -1276,4 +1276,1108 @@ def _gen_outfilename(self):\n             return os.path.abspath(self.inputs.out_file)\n         else:\n             _, name, ext = split_filename(self.inputs.in_file)\n-            return os.path.abspath(name + '_smoothed' + ext)\n\\ No newline at end of file\n+            return os.path.abspath(name + '_smoothed' + ext)\n+\n+\n+class AddXFormToHeaderInputSpec(FSTraitedSpec):\n+\n+    # required\n+    in_file = File(exists=True, mandatory=True, position=-2, argstr=\"%s\", desc=\"input volume\")\n+    # transform file does NOT need to exist at the time if using copy_name\n+    transform = File(exists=False, mandatory=True, position=-3, argstr=\"%s\", desc=\"xfm file\")\n+    out_file = File('output.mgz', position=-1, argstr=\"%s\", usedefault=True, desc=\"output volume\")\n+    # optional\n+    copy_name = traits.Bool(argstr=\"-c\", desc=\"do not try to load the xfmfile, just copy name\")\n+    verbose = traits.Bool(argstr=\"-v\", desc=\"be verbose\")\n+\n+\n+class AddXFormToHeaderOutputSpec(TraitedSpec):\n+\n+    out_file = File(exists=True, desc=\"output volume\")\n+\n+\n+class AddXFormToHeader(FSCommand):\n+    \"\"\" Just adds specified xform to the volume header\n+\n+    (!) WARNING: transform input **MUST** be an absolute path to a DataSink'ed transform or\n+    the output will reference a transform in the workflow cache directory!\n+\n+    >>> from nipype.interfaces.freesurfer import AddXFormToHeader\n+    >>> adder = AddXFormToHeader()\n+    >>> adder.inputs.in_file = 'norm.mgz'\n+    >>> adder.inputs.transform = 'talairach.xfm'\n+    >>> adder.cmdline\n+    'mri_add_xform_to_header talairach.xfm norm.mgz output.mgz'\n+\n+    >>> adder.inputs.copy_name = True\n+    >>> adder.cmdline\n+    'mri_add_xform_to_header -c talairach.xfm norm.mgz output.mgz'\n+\n+    >>> adder.run()   #doctest: +SKIP\n+\n+    References:\n+    ----------\n+    [https://surfer.nmr.mgh.harvard.edu/fswiki/mri_add_xform_to_header]\n+\n+    \"\"\"\n+    _cmd = \"mri_add_xform_to_header\"\n+    input_spec = AddXFormToHeaderInputSpec\n+    output_spec = AddXFormToHeaderOutputSpec\n+\n+    def _format_arg(self, name, spec, value):\n+        if name == 'transform':\n+            return value  # os.path.abspath(value)\n+        # if name == 'copy_name' and value:\n+        #     self.input_spec.transform\n+        return super(AddXFormToHeader, self)._format_arg(name, spec, value)\n+\n+    def _list_outputs(self):\n+        outputs = self._outputs().get()\n+        outputs[\"out_file\"] = os.path.abspath(self.inputs.out_file)\n+        return outputs\n+\n+\n+class CheckTalairachAlignmentInputSpec(FSTraitedSpec):\n+    in_file = File(argstr='-xfm %s', xor=['subject'], exists=True, mandatory=True, position=-1,\n+                   desc=\"specify the talairach.xfm file to check\")\n+    subject = traits.String(argstr='-subj %s', xor=['in_file'], mandatory=True, position=-1,\n+                            desc=\"specify subject's name\")\n+    # optional\n+    threshold = traits.Float(default=0.010, argstr='-T %.3f', desc=\"Talairach transforms for subjects with p-values <= T \" +\\\n+                             \"are considered as very unlikely default=0.010\")\n+\n+\n+class CheckTalairachAlignmentOutputSpec(TraitedSpec):\n+    out_file = traits.File(exists=True, desc=\"The input file for CheckTalairachAlignment\")\n+\n+\n+class CheckTalairachAlignment(FSCommand):\n+    \"\"\"\n+    This program detects Talairach alignment failures\n+\n+    Examples\n+    ========\n+\n+    >>> from nipype.interfaces.freesurfer import CheckTalairachAlignment\n+    >>> checker = CheckTalairachAlignment()\n+\n+    >>> checker.inputs.in_file = 'talairach.xfm'\n+    >>> checker.inputs.threshold = 0.005\n+    >>> checker.cmdline\n+    'talairach_afd -T 0.005 -xfm talairach.xfm'\n+\n+    >>> checker.run() # doctest: +SKIP\n+    \"\"\"\n+    _cmd = \"talairach_afd\"\n+    input_spec = CheckTalairachAlignmentInputSpec\n+    output_spec = CheckTalairachAlignmentOutputSpec\n+\n+    def _list_outputs(self):\n+        outputs = self.output_spec().get()\n+        outputs['out_file'] = self.inputs.in_file\n+        return outputs\n+\n+\n+class TalairachQCInputSpec(FSTraitedSpec):\n+    log_file = File(argstr='%s', mandatory=True, exists=True, position=0, desc=\"The log file for TalairachQC\")\n+\n+\n+class TalairachQC(FSScriptCommand):\n+    \"\"\"\n+    Examples\n+    ========\n+\n+    >>> from nipype.interfaces.freesurfer import TalairachQC\n+    >>> qc = TalairachQC()\n+\n+    >>> qc.inputs.log_file = 'talairach.log'\n+    >>> qc.cmdline\n+    'tal_QC_AZS talairach.log'\n+\n+    >>> qc.run() # doctest: +SKIP\n+    \"\"\"\n+    _cmd = \"tal_QC_AZS\"\n+    input_spec = TalairachQCInputSpec\n+    output_spec = FSScriptOutputSpec\n+\n+\n+class RemoveNeckInputSpec(FSTraitedSpec):\n+    in_file = File(argstr=\"%s\", exisits=True, madatory=True, position=-4, desc=\"Input file for RemoveNeck\")\n+    out_file = File(argstr=\"%s\", exists=False, mandatory=True, genfile=True, position=-1, desc=\"Output file for RemoveNeck\")\n+    transform = File(argstr=\"%s\", exists=True, mandatory=True, position=-3, desc=\"Input transform file for RemoveNeck\")\n+    template = File(argstr=\"%s\", exists=True, mandatory=True, position=-2, desc=\"Input template file for RemoveNeck\")\n+    #optional\n+    radius = traits.Int(argstr=\"-radius %d\", mandatory=False, desc=\"Radius\")\n+\n+\n+class RemoveNeckOutputSpec(TraitedSpec):\n+    out_file = File(exists=False, desc=\"Output file with neck removed\")\n+    \n+class RemoveNeck(FSCommand):\n+    \"\"\"\n+    Examples\n+    ========\n+\n+    >>> from nipype.interfaces.freesurfer import TalairachQC\n+    >>> remove_neck = RemoveNeck()\n+\n+    >>> remove_neck.inputs.in_file = 'nu.mgz'\n+    >>> remove_neck.inputs.out_file = 'nu_noneck.mgz'\n+    >>> remove_neck.run() # doctest: +SKIP\n+    \"\"\"\n+    _cmd = \"mri_remove_neck\"\n+    input_spec = RemoveNeckInputSpec\n+    output_spec = RemoveNeckOutputSpec\n+\n+    def _gen_fname(self, name):\n+        if name == 'out_file':\n+            return os.path.abspath('nu_noneck.mgz')\n+        return None\n+    \n+    def _list_outputs(self):\n+        outputs = self._outputs().get()\n+        outputs[\"out_file\"] = os.path.abspath(self.inputs.out_file)\n+        return outputs\n+\n+class MRIFillInputSpec(FSTraitedSpec):\n+    in_file = File(argstr=\"%s\", mandatory=True, exists=True, position=-2,\n+                   desc=\"Input white matter file\")\n+    out_file = File(argstr=\"%s\", mandatory=True, exists=False, position=-1,\n+                    desc=\"Output filled volume file name for MRIFill\")\n+    #optional\n+    segmentation = File(argstr=\"-segmentation %s\", mandatory=False, exists=True,\n+                        desc=\"Input segmentation file for MRIFill\")\n+    transform = File(argstr=\"-xform %s\", mandatory=False, exists=True,\n+                        desc=\"Input transform file for MRIFill\")\n+    log_file = File(argstr=\"-a %s\", mandatory=False, exists=False,\n+                        desc=\"Input segmentation file for MRIFill\")\n+    \n+class MRIFillOutputSpec(TraitedSpec):\n+    out_file = File(exists=False, desc=\"Output file from MRIFill\")\n+    \n+class MRIFill(FSCommand):\n+\n+    _cmd = \"mri_fill\"\n+    input_spec = MRIFillInputSpec\n+    output_spec = MRIFillOutputSpec\n+    \n+    def _list_outputs(self):\n+        outputs = self._outputs().get()\n+        outputs[\"out_file\"] = os.path.abspath(self.inputs.out_file)\n+        return outputs\n+\n+class ExtractMainComponentInputSpec(FSTraitedSpec):\n+    in_file = File(argstr=\"%s\", position=-2, mandatory=True, exists=True,\n+                   desc=\"Input file for ExtractMainComponent\")\n+    out_file = File(argstr=\"%s\", position=-1, mandatory=True, exists=False,\n+                   desc=\"Output file for ExtractMainComponent\")\n+    \n+class ExtractMainComponentOutputSpec(TraitedSpec):\n+    out_file = File(exists=False, desc=\"Output file for ExtractMainComponent\")\n+    ","path":"nipype/interfaces/freesurfer/utils.py","position":231,"original_position":231,"commit_id":"915eafc6877fc746e537cfd497a5ea8d1e6d88ad","original_commit_id":"915eafc6877fc746e537cfd497a5ea8d1e6d88ad","user":{"login":"chrisfilo","id":238759,"avatar_url":"https://avatars.githubusercontent.com/u/238759?v=3","gravatar_id":"","url":"https://api.github.com/users/chrisfilo","html_url":"https://github.com/chrisfilo","followers_url":"https://api.github.com/users/chrisfilo/followers","following_url":"https://api.github.com/users/chrisfilo/following{/other_user}","gists_url":"https://api.github.com/users/chrisfilo/gists{/gist_id}","starred_url":"https://api.github.com/users/chrisfilo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chrisfilo/subscriptions","organizations_url":"https://api.github.com/users/chrisfilo/orgs","repos_url":"https://api.github.com/users/chrisfilo/repos","events_url":"https://api.github.com/users/chrisfilo/events{/privacy}","received_events_url":"https://api.github.com/users/chrisfilo/received_events","type":"User","site_admin":false},"body":"![Codacy](https://www.codacy.com/versioned/images/favicon.png) Issue found: [class already defined line 1175](https://www.codacy.com/app/krzysztof-gorgolewski/nipy_nipype/file/825382778/issues/source?bid=2767207&fileBranchId=2768049#l1478)","created_at":"2015-08-02T08:06:11Z","updated_at":"2015-08-02T08:06:11Z","html_url":"https://github.com/nipy/nipype/pull/1116#discussion_r36040691","pull_request_url":"https://api.github.com/repos/nipy/nipype/pulls/1116","_links":{"self":{"href":"https://api.github.com/repos/nipy/nipype/pulls/comments/36040691"},"html":{"href":"https://github.com/nipy/nipype/pull/1116#discussion_r36040691"},"pull_request":{"href":"https://api.github.com/repos/nipy/nipype/pulls/1116"}}},"pull_request":{"url":"https://api.github.com/repos/nipy/nipype/pulls/1116","id":37615919,"html_url":"https://github.com/nipy/nipype/pull/1116","diff_url":"https://github.com/nipy/nipype/pull/1116.diff","patch_url":"https://github.com/nipy/nipype/pull/1116.patch","issue_url":"https://api.github.com/repos/nipy/nipype/issues/1116","number":1116,"state":"open","locked":false,"title":"Freesurfer longitudinal:  REVIEW ONLY","user":{"login":"hjmjohnson","id":313970,"avatar_url":"https://avatars.githubusercontent.com/u/313970?v=3","gravatar_id":"","url":"https://api.github.com/users/hjmjohnson","html_url":"https://github.com/hjmjohnson","followers_url":"https://api.github.com/users/hjmjohnson/followers","following_url":"https://api.github.com/users/hjmjohnson/following{/other_user}","gists_url":"https://api.github.com/users/hjmjohnson/gists{/gist_id}","starred_url":"https://api.github.com/users/hjmjohnson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hjmjohnson/subscriptions","organizations_url":"https://api.github.com/users/hjmjohnson/orgs","repos_url":"https://api.github.com/users/hjmjohnson/repos","events_url":"https://api.github.com/users/hjmjohnson/events{/privacy}","received_events_url":"https://api.github.com/users/hjmjohnson/received_events","type":"User","site_admin":false},"body":"DO NOT INCLUDE THIS!  It is only for review.  This branch should be deleted and  updated later.\r\n\r\n","created_at":"2015-06-13T00:51:48Z","updated_at":"2015-08-02T08:06:11Z","closed_at":null,"merged_at":null,"merge_commit_sha":"cb4484085b02df01e2eb3ef8971b58c43522727b","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/nipy/nipype/pulls/1116/commits","review_comments_url":"https://api.github.com/repos/nipy/nipype/pulls/1116/comments","review_comment_url":"https://api.github.com/repos/nipy/nipype/pulls/comments{/number}","comments_url":"https://api.github.com/repos/nipy/nipype/issues/1116/comments","statuses_url":"https://api.github.com/repos/nipy/nipype/statuses/915eafc6877fc746e537cfd497a5ea8d1e6d88ad","head":{"label":"BRAINSia:freesurfer_longitudinal","ref":"freesurfer_longitudinal","sha":"915eafc6877fc746e537cfd497a5ea8d1e6d88ad","user":{"login":"BRAINSia","id":811110,"avatar_url":"https://avatars.githubusercontent.com/u/811110?v=3","gravatar_id":"","url":"https://api.github.com/users/BRAINSia","html_url":"https://github.com/BRAINSia","followers_url":"https://api.github.com/users/BRAINSia/followers","following_url":"https://api.github.com/users/BRAINSia/following{/other_user}","gists_url":"https://api.github.com/users/BRAINSia/gists{/gist_id}","starred_url":"https://api.github.com/users/BRAINSia/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/BRAINSia/subscriptions","organizations_url":"https://api.github.com/users/BRAINSia/orgs","repos_url":"https://api.github.com/users/BRAINSia/repos","events_url":"https://api.github.com/users/BRAINSia/events{/privacy}","received_events_url":"https://api.github.com/users/BRAINSia/received_events","type":"Organization","site_admin":false},"repo":{"id":2350556,"name":"nipype","full_name":"BRAINSia/nipype","owner":{"login":"BRAINSia","id":811110,"avatar_url":"https://avatars.githubusercontent.com/u/811110?v=3","gravatar_id":"","url":"https://api.github.com/users/BRAINSia","html_url":"https://github.com/BRAINSia","followers_url":"https://api.github.com/users/BRAINSia/followers","following_url":"https://api.github.com/users/BRAINSia/following{/other_user}","gists_url":"https://api.github.com/users/BRAINSia/gists{/gist_id}","starred_url":"https://api.github.com/users/BRAINSia/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/BRAINSia/subscriptions","organizations_url":"https://api.github.com/users/BRAINSia/orgs","repos_url":"https://api.github.com/users/BRAINSia/repos","events_url":"https://api.github.com/users/BRAINSia/events{/privacy}","received_events_url":"https://api.github.com/users/BRAINSia/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/BRAINSia/nipype","description":"Workflows 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