{"action":"created","comment":{"url":"https://api.github.com/repos/nidata/nidata/pulls/comments/56737529","id":56737529,"diff_hunk":"@@ -144,88 +145,265 @@ def get_subject_list(self, n_subjects=None):\n \n         return subject_ids[:n_subjects]\n \n-    def get_files(self, data_type, volume_type, subj_id):\n-        assert subj_id is not None and subj_id != ''\n+    def get_diff_files(self, process, subj_id):\n+        files = []\n+\n+        if not process:\n+            diff_path = '%s/unprocessed/3T/Diffusion' % subj_id\n+\n+            files += ['%s/%s_3T_BIAS_32CH.nii.gz' % (diff_path, subj_id)]\n+            files += ['%s/%s_3T_BIAS_BC.nii.gz' % (diff_path, subj_id)]\n+            files += ['%s/%s_3T_DWI_dir95_LR_SBRef.nii.gz' % (diff_path, subj_id)]\n+            files += ['%s/%s_3T_DWI_dir95_LR.bval' % (diff_path, subj_id)]\n+            files += ['%s/%s_3T_DWI_dir95_LR.bvec' % (diff_path, subj_id)]\n+            files += ['%s/%s_3T_DWI_dir95_LR.nii.gz' % (diff_path, subj_id)]\n+            files += ['%s/%s_3T_DWI_dir95_RL_SBRef.nii.gz' % (diff_path, subj_id)]\n+            files += ['%s/%s_3T_DWI_dir95_RL.bval' % (diff_path, subj_id)]\n+            files += ['%s/%s_3T_DWI_dir95_RL.bvec' % (diff_path, subj_id)]\n+            files += ['%s/%s_3T_DWI_dir95_RL.nii.gz' % (diff_path, subj_id)]\n+\n+            files += ['%s/release-notes/Diffusion_unproc.txt' % subj_id]\n+        else:\n+            diff_path = '%s/T1w/Diffusion' % subj_id\n+\n+            files += ['%s/bvals' % diff_path]\n+            files += ['%s/bvecs' % diff_path]\n+            files += ['%s/data.nii.gz' % diff_path]\n+\n+            files += ['%s/release-notes/Diffusion_preproc.txt' % subj_id]\n+        return files\n+\n+    def get_anat_files(self, process, subj_id, atlas, mni, property):\n+        files = []\n+\n+        if not process:\n+            anat_path = '%s/unprocessed/3T' % subj_id\n \n-        if self.fetcher_type == 'aws':\n-            # S3 bucket specific layout\n-            subj_path = '{subj_id}'\n-        else:  # xnat/http\n-            subj_path = ('{subj_id}/experiments/{subj_id}_CREST/resources/'\n-                         '{subj_id}_CREST/files')\n+            files += ['%s/T1w_MPR1/%s_3T_AFI.nii.gz' % (anat_path, subj_id)]\n+            files += ['%s/T1w_MPR1/%s_3T_BIAS_32CH.nii.gz' % (anat_path, subj_id)]\n+            files += ['%s/T1w_MPR1/%s_3T_BIAS_BC.nii.gz' % (anat_path, subj_id)]\n+            files += ['%s/T1w_MPR1/%s_3T_FieldMap_Magnitude.nii.gz' % (anat_path, subj_id)]\n+            files += ['%s/T1w_MPR1/%s_3T_FieldMap_Phase.nii.gz' % (anat_path, subj_id)]\n+            files += ['%s/T1w_MPR1/%s_3T_T1w_MPR1.nii.gz' % (anat_path, subj_id)]\n+\n+            files += ['%s/release-notes/Structural_unproc.txt' % subj_id]\n+        else:\n+            if not mni:\n+                if atlas == 'native':\n+                    anat_path = '%s/T1w/Native' % subj_id\n+                    if property == 'thickness':\n+                        files += ['%s/%s.L.midthickness.native.surf.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.R.midthickness.native.surf.gii' % (anat_path, subj_id)]\n+                elif atlas == 'fsaverage':\n+                    anat_path = '%s/T1w/fsaverage_LR32k' % subj_id\n+                    if property == 'thickness':\n+                        files += ['%s/%s.L.midthickness.32k_fs_LR.surf.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.R.midthickness.32k_fs_LR.surf.gii' % (anat_path, subj_id)]\n+            else:\n+                if atlas == 'native':\n+                    anat_path = '%s/MNINonLinear/Native' % subj_id\n+                    if property == 'thickness':\n+                        files += ['%s/%s.corrThickness.native.dscalar.nii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.L.corrThickness.native.shape.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.L.midthickness.native.surf.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.L.thickness.native.shape.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.R.corrThickness.native.shape.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.R.midthickness.native.surf.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.R.thickness.native.shape.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.thickness.native.dscalar.nii' % (anat_path, subj_id)]\n+                    elif property == 'curvature':\n+                        files += ['%s/%s.curvature.native.dscalar.nii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.L.curvature.native.shape.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.R.curvature.native.shape.gii' % (anat_path, subj_id)]\n+                    elif property == 'myelinmap':\n+                        files += ['%s/%s.L.MyelinMap.native.func.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.L.MyelinMap_BC.native.func.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.L.SmoothedMyelinMap.native.func.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.L.SmoothedMyelinMap_BC.native.func.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.MyelinMap.native.dscalar.nii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.MyelinMap_BC.native.dscalar.nii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.R.MyelinMap.native.func.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.R.MyelinMap_BC.native.func.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.R.SmoothedMyelinMap.native.func.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.R.SmoothedMyelinMap_BC.native.func.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.SmoothedMyelinMap.native.dscalar.nii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.SmoothedMyelinMap_BC.native.dscalar.nii' % (anat_path, subj_id)]\n+                elif atlas == 'fsaverage':\n+                    anat_path = '%s/MNINonLinear/fsaverage_LR32k' % subj_id\n+                    if property == 'thickness':\n+                        files += ['%s/%s.corrThickness.32k_fs_LR.dscalar.nii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.L.corrThickness.32k_fs_LR.shape.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.L.midthickness.32k_fs_LR.surf.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.L.thickness.32k_fs_LR.shape.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.R.corrThickness.32k_fs_LR.shape.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.R.midthickness.32k_fs_LR.surf.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.R.thickness.32k_fs_LR.shape.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.thickness.32k_fs_LR.dscalar.nii' % (anat_path, subj_id)]\n+                    elif property == 'curvature':\n+                        files += ['%s/%s.curvature.32k_fs_LR.dscalar.nii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.L.curvature.32k_fs_LR.shape.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.R.curvature.32k_fs_LR.shape.gii' % (anat_path, subj_id)]\n+                    elif property == 'myelinmap':\n+                        files += ['%s/%s.L.MyelinMap.32k_fs_LR.func.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.L.MyelinMap_BC.32k_fs_LR.func.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.L.SmoothedMyelinMap.32k_fs_LR.func.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.L.SmoothedMyelinMap_BC.32k_fs_LR.func.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.MyelinMap.32k_fs_LR.dscalar.nii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.MyelinMap_BC.32k_fs_LR.dscalar.nii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.R.MyelinMap.32k_fs_LR.func.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.R.MyelinMap_BC.32k_fs_LR.func.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.R.SmoothedMyelinMap.32k_fs_LR.func.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.R.SmoothedMyelinMap_BC.32k_fs_LR.func.gii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.SmoothedMyelinMap.32k_fs_LR.dscalar.nii' % (anat_path, subj_id)]\n+                        files += ['%s/%s.SmoothedMyelinMap_BC.32k_fs_LR.dscalar.nii' % (anat_path, subj_id)]\n+\n+            files += ['%s/release-notes/Structural_preproc.txt']\n+        return files\n \n+    def get_rest_files(self, process, subj_id):\n         files = []\n \n-        if volume_type == '3T' and data_type == 'anat':\n-            anat_path = '%s/unprocessed/3T' % subj_path\n-            files += [('%s/%s' % (anat_path, fil))\n-                      .format(stype=stype, subj_id=subj_id)\n-                      for stype in ['T1w_MPR1', 'T2w_SPC1']\n-                      for fil in [\n-                          '{stype}/{subj_id}_3T_AFI.nii.gz',\n-                          '{stype}/{subj_id}_3T_BIAS_32CH.nii.gz',\n-                          '{stype}/{subj_id}_3T_BIAS_BC.nii.gz',\n-                          '{stype}/{subj_id}_3T_FieldMap_Magnitude.nii.gz',\n-                          '{stype}/{subj_id}_3T_FieldMap_Phase.nii.gz',\n-                          '{stype}/{subj_id}_3T_{stype}.nii.gz']]\n-\n-        elif volume_type == '3T' and data_type == 'diff':\n-            diff_path = '%s/unprocessed/3T/Diffusion' % subj_path\n-            files += [('%s/%s' % (diff_path, fil))\n-                      .format(subj_id=subj_id, n_dirs=n_dirs)\n-                      for n_dirs in [95]  # 96? 97?\n-                      for fil in [\n-                          '{subj_id}_3T_BIAS_32CH.nii.gz',\n-                          '{subj_id}_3T_BIAS_BC.nii.gz',\n-                          '{subj_id}_3T_DWI_dir{n_dirs}_LR.nii.gz',\n-                          '{subj_id}_3T_DWI_dir{n_dirs}_LR.bval',\n-                          '{subj_id}_3T_DWI_dir{n_dirs}_LR.bvec',\n-                          '{subj_id}_3T_DWI_dir{n_dirs}_RL_SBRef.nii.gz']]\n-\n-        elif volume_type == '3T' and data_type == 'func':\n-            rest_path = '%s/unprocessed/3T' % subj_path\n-            files += [('%s/tfMRI_{scan}_{direction}/%s' % (rest_path, fil))\n-                      .format(subj_id=subj_id, scan=scan, direction=direction)\n-                      for scan in ['EMOTION', 'GAMBLING', 'LANGUAGE', 'MOTOR',\n-                                   'RELATIONAL', 'SOCIAL', 'WM']\n-                      for direction in ['LR', 'RL']\n-                      for fil in [\n-                          '{subj_id}_3T_BIAS_32CH.nii.gz',\n-                          '{subj_id}_3T_BIAS_BC.nii.gz',\n-                          '{subj_id}_3T_tfMRI_{scan}_{direction}_SBRef.nii.gz',\n-                          '{subj_id}_3T_tfMRI_{scan}_{direction}.nii.gz',\n-                          '{subj_id}_3T_SpinEchoFieldMap_LR.nii.gz',\n-                          '{subj_id}_3T_SpinEchoFieldMap_RL.nii.gz']]\n-\n-        elif volume_type == '3T' and data_type == 'rest':\n-            func_path = '%s/unprocessed/3T' % subj_path\n-            files += [('%s/rfMRI_{scan}_{direction}/%s' % (func_path, fil))\n-                      .format(subj_id=subj_id, scan=scan, direction=direction)\n-                      for scan in ['REST1', 'REST2']\n-                      for direction in ['LR', 'RL']\n-                      for fil in [\n-                          '{subj_id}_3T_BIAS_32CH.nii.gz',\n-                          '{subj_id}_3T_BIAS_BC.nii.gz',\n-                          '{subj_id}_3T_rfMRI_{scan}_{direction}_SBRef.nii.gz',\n-                          '{subj_id}_3T_rfMRI_{scan}_{direction}.nii.gz',\n-                          '{subj_id}_3T_SpinEchoFieldMap_LR.nii.gz',\n-                          '{subj_id}_3T_SpinEchoFieldMap_RL.nii.gz']]\n+        if not process:\n+            rest_path = '%s/unprocessed/3T' % subj_id\n \n+            files += ['%s/rfMRI_REST1_LR/%s_3T_BIAS_32CH.nii.gz' % (rest_path, subj_id)]\n+            files += ['%s/rfMRI_REST1_LR/%s_3T_BIAS_BC.nii.gz' % (rest_path, subj_id)]\n+            files += ['%s/rfMRI_REST1_LR/%s_3T_rfMRI_REST1_LR_SBRef.nii.gz' % (rest_path, subj_id)]\n+            files += ['%s/rfMRI_REST1_LR/%s_3T_rfMRI_REST1_LR.nii.gz' % (rest_path, subj_id)]\n+            files += ['%s/rfMRI_REST1_LR/%s_3T_SpinEchoFieldMap_LR.nii.gz' % (rest_path, subj_id)]\n+            files += ['%s/rfMRI_REST1_LR/%s_3T_SpinEchoFieldMap_RL.nii.gz' % (rest_path, subj_id)]\n+            files += ['%s/rfMRI_REST1_LR/LINKED_DATA/PHYSIO/%s_3T_rfMRI_REST1_LR_Physio_log.txt' % (rest_path, subj_id)]\n+\n+            files += ['%s/release-notes/rfMRI_REST1_unproc.txt' % subj_id]\n+            files += ['%s/release-notes/rfMRI_REST2_unproc.txt' % subj_id]\n         else:\n-            raise NotImplementedError(\"Cannot (yet!) fetch '%s' files\" % (\n-                volume_type))\n+            rest_path = '%s/MNINonLinear/Results' % subj_id\n+            files += ['%s/rfMRI_REST1_LR/brainmask_fs.2.nii.gz' % rest_path]\n+            files += ['%s/rfMRI_REST1_LR/Movement_Regressors_dt.txt' % rest_path]\n+            files += ['%s/rfMRI_REST1_LR/Movement_Regressors.txt' % rest_path]\n+            files += ['%s/rfMRI_REST1_LR/Movement_AbsoluteRMS.txt' % rest_path]\n+            files += ['%s/rfMRI_REST1_LR/Movement_AbsoluteRMS_mean.txt' % rest_path]\n+            files += ['%s/rfMRI_REST1_LR/Movement_RelativeRMS.txt' % rest_path]\n+            files += ['%s/rfMRI_REST1_LR/Movement_RelativeRMS_mean.txt' % rest_path]\n+            files += ['%s/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseries.nii' % rest_path]\n+            files += ['%s/rfMRI_REST1_LR/rfMRI_REST1_LR_Jacobian.nii.gz' % rest_path]\n+            files += ['%s/rfMRI_REST1_LR/rfMRI_REST1_LR_SBRef.nii.gz' % rest_path]\n+            files += ['%s/rfMRI_REST1_LR/rfMRI_REST1_LR.nii.gz' % rest_path]\n+            files += ['%s/rfMRI_REST1_LR/rfMRI_REST1_LR_Physio_log.txt' % rest_path]\n+            files += ['%s/rfMRI_REST1_LR/RibbonVolumeToSurfaceMapping/goodvoxels.nii.gz' % rest_path]\n+\n+            files += ['%s/release-notes/rfMRI_REST1_preproc.txt' % subj_id]\n+            files += ['%s/release-notes/rfMRI_REST2_preproc.txt' % subj_id]","path":"nidata/multimodal/hcp/__init__.py","position":242,"original_position":242,"commit_id":"c3adc81e0e120c0d9674a404687dedbc36a27631","original_commit_id":"c3adc81e0e120c0d9674a404687dedbc36a27631","user":{"login":"bcipolli","id":4072455,"avatar_url":"https://avatars.githubusercontent.com/u/4072455?v=3","gravatar_id":"","url":"https://api.github.com/users/bcipolli","html_url":"https://github.com/bcipolli","followers_url":"https://api.github.com/users/bcipolli/followers","following_url":"https://api.github.com/users/bcipolli/following{/other_user}","gists_url":"https://api.github.com/users/bcipolli/gists{/gist_id}","starred_url":"https://api.github.com/users/bcipolli/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bcipolli/subscriptions","organizations_url":"https://api.github.com/users/bcipolli/orgs","repos_url":"https://api.github.com/users/bcipolli/repos","events_url":"https://api.github.com/users/bcipolli/events{/privacy}","received_events_url":"https://api.github.com/users/bcipolli/received_events","type":"User","site_admin":false},"body":"You should either include all `REST1` and `REST2` files, or only keep one `release-notes` file.","created_at":"2016-03-18T23:54:46Z","updated_at":"2016-03-18T23:54:46Z","html_url":"https://github.com/nidata/nidata/pull/79#discussion_r56737529","pull_request_url":"https://api.github.com/repos/nidata/nidata/pulls/79","_links":{"self":{"href":"https://api.github.com/repos/nidata/nidata/pulls/comments/56737529"},"html":{"href":"https://github.com/nidata/nidata/pull/79#discussion_r56737529"},"pull_request":{"href":"https://api.github.com/repos/nidata/nidata/pulls/79"}}},"pull_request":{"url":"https://api.github.com/repos/nidata/nidata/pulls/79","id":61804573,"html_url":"https://github.com/nidata/nidata/pull/79","diff_url":"https://github.com/nidata/nidata/pull/79.diff","patch_url":"https://github.com/nidata/nidata/pull/79.patch","issue_url":"https://api.github.com/repos/nidata/nidata/issues/79","number":79,"state":"open","locked":false,"title":"Added diffusion file fetcher function","user":{"login":"hwd15508","id":12350554,"avatar_url":"https://avatars.githubusercontent.com/u/12350554?v=3","gravatar_id":"","url":"https://api.github.com/users/hwd15508","html_url":"https://github.com/hwd15508","followers_url":"https://api.github.com/users/hwd15508/followers","following_url":"https://api.github.com/users/hwd15508/following{/other_user}","gists_url":"https://api.github.com/users/hwd15508/gists{/gist_id}","starred_url":"https://api.github.com/users/hwd15508/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hwd15508/subscriptions","organizations_url":"https://api.github.com/users/hwd15508/orgs","repos_url":"https://api.github.com/users/hwd15508/repos","events_url":"https://api.github.com/users/hwd15508/events{/privacy}","received_events_url":"https://api.github.com/users/hwd15508/received_events","type":"User","site_admin":false},"body":"-Added function to fetch diffusion files\r\n-Changed profile_name default to 'hcp' instead of None\r\n-Changed fetcher_type to 'aws' instead of 'http'\r\n@bcipolli 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