Generate CIFTI and TSV versions of coverage, timeseries, and correlat…

…ion files (#785)

.github/ISSUE_TEMPLATE/config.yml

@@ -1,4 +1,4 @@
 contact_links:
   - name: Usage question
-    url: https://neurostars.org/tag/xcp_d
+    url: https://neurostars.org/tags/c/software-support/234/xcp_d
     about: Please ask questions about using xcp_d on NeuroStars.

.gitignore

@@ -15,7 +15,6 @@ xcp_d/data/ds001419-example.tar.gz
 xcp_surface/.DS_Store
 .DS_Store
 *.pyc
-*.tsv
 *.pyc
 .eggs
 .Rhistory

docs/usage.rst

@@ -429,5 +429,5 @@ The documentation of this project is found here: https://xcp-d.readthedocs.io/.
 All bugs, concerns and enhancement requests for this software can be submitted here:
 https://github.com/PennLINC/xcp_d/issues.
 
-If you have a question about using ``xcp_d``, please create a new topic on `NeuroStars <https://neurostars.org>`_ with the `"xcp_d" tag <https://neurostars.org/tag/xcp_d>`_.
+If you have a question about using ``xcp_d``, please create a new topic on `NeuroStars <https://neurostars.org>`_ with `the "Software Support" category and the "xcp_d" tag <https://neurostars.org/tags/c/software-support/234/xcp_d>`_.
 The ``xcp_d`` developers follow NeuroStars, and will be able to answer your question there.

xcp_d/data/ciftiatlas/Glasser_360Parcels_info.tsv

@@ -0,0 +1,361 @@
+index	name	cifti_name
+1	Right_V1	R_V1_ROI
+2	Right_MST	R_MST_ROI
+3	Right_V6	R_V6_ROI
+4	Right_V2	R_V2_ROI
+5	Right_V3	R_V3_ROI
+6	Right_V4	R_V4_ROI
+7	Right_V8	R_V8_ROI
+8	Right_4	R_4_ROI
+9	Right_3b	R_3b_ROI
+10	Right_FEF	R_FEF_ROI
+11	Right_PEF	R_PEF_ROI
+12	Right_55b	R_55b_ROI
+13	Right_V3A	R_V3A_ROI
+14	Right_RSC	R_RSC_ROI
+15	Right_POS2	R_POS2_ROI
+16	Right_V7	R_V7_ROI
+17	Right_IPS1	R_IPS1_ROI
+18	Right_FFC	R_FFC_ROI
+19	Right_V3B	R_V3B_ROI
+20	Right_LO1	R_LO1_ROI
+21	Right_LO2	R_LO2_ROI
+22	Right_PIT	R_PIT_ROI
+23	Right_MT	R_MT_ROI
+24	Right_A1	R_A1_ROI
+25	Right_PSL	R_PSL_ROI
+26	Right_SFL	R_SFL_ROI
+27	Right_PCV	R_PCV_ROI
+28	Right_STV	R_STV_ROI
+29	Right_7Pm	R_7Pm_ROI
+30	Right_7m	R_7m_ROI
+31	Right_POS1	R_POS1_ROI
+32	Right_23d	R_23d_ROI
+33	Right_v23ab	R_v23ab_ROI
+34	Right_d23ab	R_d23ab_ROI
+35	Right_31pv	R_31pv_ROI
+36	Right_5m	R_5m_ROI
+37	Right_5mv	R_5mv_ROI
+38	Right_23c	R_23c_ROI
+39	Right_5L	R_5L_ROI
+40	Right_24dd	R_24dd_ROI
+41	Right_24dv	R_24dv_ROI
+42	Right_7AL	R_7AL_ROI
+43	Right_SCEF	R_SCEF_ROI
+44	Right_6ma	R_6ma_ROI
+45	Right_7Am	R_7Am_ROI
+46	Right_7PL	R_7PL_ROI
+47	Right_7PC	R_7PC_ROI
+48	Right_LIPv	R_LIPv_ROI
+49	Right_VIP	R_VIP_ROI
+50	Right_MIP	R_MIP_ROI
+51	Right_1	R_1_ROI
+52	Right_2	R_2_ROI
+53	Right_3a	R_3a_ROI
+54	Right_6d	R_6d_ROI
+55	Right_6mp	R_6mp_ROI
+56	Right_6v	R_6v_ROI
+57	Right_p24pr	R_p24pr_ROI
+58	Right_33pr	R_33pr_ROI
+59	Right_a24pr	R_a24pr_ROI
+60	Right_p32pr	R_p32pr_ROI
+61	Right_a24	R_a24_ROI
+62	Right_d32	R_d32_ROI
+63	Right_8BM	R_8BM_ROI
+64	Right_p32	R_p32_ROI
+65	Right_10r	R_10r_ROI
+66	Right_47m	R_47m_ROI
+67	Right_8Av	R_8Av_ROI
+68	Right_8Ad	R_8Ad_ROI
+69	Right_9m	R_9m_ROI
+70	Right_8BL	R_8BL_ROI
+71	Right_9p	R_9p_ROI
+72	Right_10d	R_10d_ROI
+73	Right_8C	R_8C_ROI
+74	Right_44	R_44_ROI
+75	Right_45	R_45_ROI
+76	Right_47l	R_47l_ROI
+77	Right_a47r	R_a47r_ROI
+78	Right_6r	R_6r_ROI
+79	Right_IFJa	R_IFJa_ROI
+80	Right_IFJp	R_IFJp_ROI
+81	Right_IFSp	R_IFSp_ROI
+82	Right_IFSa	R_IFSa_ROI
+83	Right_p9-46v	R_p9-46v_ROI
+84	Right_46	R_46_ROI
+85	Right_a9-46v	R_a9-46v_ROI
+86	Right_9-46d	R_9-46d_ROI
+87	Right_9a	R_9a_ROI
+88	Right_10v	R_10v_ROI
+89	Right_a10p	R_a10p_ROI
+90	Right_10pp	R_10pp_ROI
+91	Right_11l	R_11l_ROI
+92	Right_13l	R_13l_ROI
+93	Right_OFC	R_OFC_ROI
+94	Right_47s	R_47s_ROI
+95	Right_LIPd	R_LIPd_ROI
+96	Right_6a	R_6a_ROI
+97	Right_i6-8	R_i6-8_ROI
+98	Right_s6-8	R_s6-8_ROI
+99	Right_43	R_43_ROI
+100	Right_OP4	R_OP4_ROI
+101	Right_OP1	R_OP1_ROI
+102	Right_OP2-3	R_OP2-3_ROI
+103	Right_52	R_52_ROI
+104	Right_RI	R_RI_ROI
+105	Right_PFcm	R_PFcm_ROI
+106	Right_PoI2	R_PoI2_ROI
+107	Right_TA2	R_TA2_ROI
+108	Right_FOP4	R_FOP4_ROI
+109	Right_MI	R_MI_ROI
+110	Right_Pir	R_Pir_ROI
+111	Right_AVI	R_AVI_ROI
+112	Right_AAIC	R_AAIC_ROI
+113	Right_FOP1	R_FOP1_ROI
+114	Right_FOP3	R_FOP3_ROI
+115	Right_FOP2	R_FOP2_ROI
+116	Right_PFt	R_PFt_ROI
+117	Right_AIP	R_AIP_ROI
+118	Right_EC	R_EC_ROI
+119	Right_PreS	R_PreS_ROI
+120	Right_H	R_H_ROI
+121	Right_ProS	R_ProS_ROI
+122	Right_PeEc	R_PeEc_ROI
+123	Right_STGa	R_STGa_ROI
+124	Right_PBelt	R_PBelt_ROI
+125	Right_A5	R_A5_ROI
+126	Right_PHA1	R_PHA1_ROI
+127	Right_PHA3	R_PHA3_ROI
+128	Right_STSda	R_STSda_ROI
+129	Right_STSdp	R_STSdp_ROI
+130	Right_STSvp	R_STSvp_ROI
+131	Right_TGd	R_TGd_ROI
+132	Right_TE1a	R_TE1a_ROI
+133	Right_TE1p	R_TE1p_ROI
+134	Right_TE2a	R_TE2a_ROI
+135	Right_TF	R_TF_ROI
+136	Right_TE2p	R_TE2p_ROI
+137	Right_PHT	R_PHT_ROI
+138	Right_PH	R_PH_ROI
+139	Right_TPOJ1	R_TPOJ1_ROI
+140	Right_TPOJ2	R_TPOJ2_ROI
+141	Right_TPOJ3	R_TPOJ3_ROI
+142	Right_DVT	R_DVT_ROI
+143	Right_PGp	R_PGp_ROI
+144	Right_IP2	R_IP2_ROI
+145	Right_IP1	R_IP1_ROI
+146	Right_IP0	R_IP0_ROI
+147	Right_PFop	R_PFop_ROI
+148	Right_PF	R_PF_ROI
+149	Right_PFm	R_PFm_ROI
+150	Right_PGi	R_PGi_ROI
+151	Right_PGs	R_PGs_ROI
+152	Right_V6A	R_V6A_ROI
+153	Right_VMV1	R_VMV1_ROI
+154	Right_VMV3	R_VMV3_ROI
+155	Right_PHA2	R_PHA2_ROI
+156	Right_V4t	R_V4t_ROI
+157	Right_FST	R_FST_ROI
+158	Right_V3CD	R_V3CD_ROI
+159	Right_LO3	R_LO3_ROI
+160	Right_VMV2	R_VMV2_ROI
+161	Right_31pd	R_31pd_ROI
+162	Right_31a	R_31a_ROI
+163	Right_VVC	R_VVC_ROI
+164	Right_25	R_25_ROI
+165	Right_s32	R_s32_ROI
+166	Right_pOFC	R_pOFC_ROI
+167	Right_PoI1	R_PoI1_ROI
+168	Right_Ig	R_Ig_ROI
+169	Right_FOP5	R_FOP5_ROI
+170	Right_p10p	R_p10p_ROI
+171	Right_p47r	R_p47r_ROI
+172	Right_TGv	R_TGv_ROI
+173	Right_MBelt	R_MBelt_ROI
+174	Right_LBelt	R_LBelt_ROI
+175	Right_A4	R_A4_ROI
+176	Right_STSva	R_STSva_ROI
+177	Right_TE1m	R_TE1m_ROI
+178	Right_PI	R_PI_ROI
+179	Right_a32pr	R_a32pr_ROI
+180	Right_p24	R_p24_ROI
+181	Left_V1	L_V1_ROI
+182	Left_MST	L_MST_ROI
+183	Left_V6	L_V6_ROI
+184	Left_V2	L_V2_ROI
+185	Left_V3	L_V3_ROI
+186	Left_V4	L_V4_ROI
+187	Left_V8	L_V8_ROI
+188	Left_4	L_4_ROI
+189	Left_3b	L_3b_ROI
+190	Left_FEF	L_FEF_ROI
+191	Left_PEF	L_PEF_ROI
+192	Left_55b	L_55b_ROI
+193	Left_V3A	L_V3A_ROI
+194	Left_RSC	L_RSC_ROI
+195	Left_POS2	L_POS2_ROI
+196	Left_V7	L_V7_ROI
+197	Left_IPS1	L_IPS1_ROI
+198	Left_FFC	L_FFC_ROI
+199	Left_V3B	L_V3B_ROI
+200	Left_LO1	L_LO1_ROI
+201	Left_LO2	L_LO2_ROI
+202	Left_PIT	L_PIT_ROI
+203	Left_MT	L_MT_ROI
+204	Left_A1	L_A1_ROI
+205	Left_PSL	L_PSL_ROI
+206	Left_SFL	L_SFL_ROI
+207	Left_PCV	L_PCV_ROI
+208	Left_STV	L_STV_ROI
+209	Left_7Pm	L_7Pm_ROI
+210	Left_7m	L_7m_ROI
+211	Left_POS1	L_POS1_ROI
+212	Left_23d	L_23d_ROI
+213	Left_v23ab	L_v23ab_ROI
+214	Left_d23ab	L_d23ab_ROI
+215	Left_31pv	L_31pv_ROI
+216	Left_5m	L_5m_ROI
+217	Left_5mv	L_5mv_ROI
+218	Left_23c	L_23c_ROI
+219	Left_5L	L_5L_ROI
+220	Left_24dd	L_24dd_ROI
+221	Left_24dv	L_24dv_ROI
+222	Left_7AL	L_7AL_ROI
+223	Left_SCEF	L_SCEF_ROI
+224	Left_6ma	L_6ma_ROI
+225	Left_7Am	L_7Am_ROI
+226	Left_7PL	L_7PL_ROI
+227	Left_7PC	L_7PC_ROI
+228	Left_LIPv	L_LIPv_ROI
+229	Left_VIP	L_VIP_ROI
+230	Left_MIP	L_MIP_ROI
+231	Left_1	L_1_ROI
+232	Left_2	L_2_ROI
+233	Left_3a	L_3a_ROI
+234	Left_6d	L_6d_ROI
+235	Left_6mp	L_6mp_ROI
+236	Left_6v	L_6v_ROI
+237	Left_p24pr	L_p24pr_ROI
+238	Left_33pr	L_33pr_ROI
+239	Left_a24pr	L_a24pr_ROI
+240	Left_p32pr	L_p32pr_ROI
+241	Left_a24	L_a24_ROI
+242	Left_d32	L_d32_ROI
+243	Left_8BM	L_8BM_ROI
+244	Left_p32	L_p32_ROI
+245	Left_10r	L_10r_ROI
+246	Left_47m	L_47m_ROI
+247	Left_8Av	L_8Av_ROI
+248	Left_8Ad	L_8Ad_ROI
+249	Left_9m	L_9m_ROI
+250	Left_8BL	L_8BL_ROI
+251	Left_9p	L_9p_ROI
+252	Left_10d	L_10d_ROI
+253	Left_8C	L_8C_ROI
+254	Left_44	L_44_ROI
+255	Left_45	L_45_ROI
+256	Left_47l	L_47l_ROI
+257	Left_a47r	L_a47r_ROI
+258	Left_6r	L_6r_ROI
+259	Left_IFJa	L_IFJa_ROI
+260	Left_IFJp	L_IFJp_ROI
+261	Left_IFSp	L_IFSp_ROI
+262	Left_IFSa	L_IFSa_ROI
+263	Left_p9-46v	L_p9-46v_ROI
+264	Left_46	L_46_ROI
+265	Left_a9-46v	L_a9-46v_ROI
+266	Left_9-46d	L_9-46d_ROI
+267	Left_9a	L_9a_ROI
+268	Left_10v	L_10v_ROI
+269	Left_a10p	L_a10p_ROI
+270	Left_10pp	L_10pp_ROI
+271	Left_11l	L_11l_ROI
+272	Left_13l	L_13l_ROI
+273	Left_OFC	L_OFC_ROI
+274	Left_47s	L_47s_ROI
+275	Left_LIPd	L_LIPd_ROI
+276	Left_6a	L_6a_ROI
+277	Left_i6-8	L_i6-8_ROI
+278	Left_s6-8	L_s6-8_ROI
+279	Left_43	L_43_ROI
+280	Left_OP4	L_OP4_ROI
+281	Left_OP1	L_OP1_ROI
+282	Left_OP2-3	L_OP2-3_ROI
+283	Left_52	L_52_ROI
+284	Left_RI	L_RI_ROI
+285	Left_PFcm	L_PFcm_ROI
+286	Left_PoI2	L_PoI2_ROI
+287	Left_TA2	L_TA2_ROI
+288	Left_FOP4	L_FOP4_ROI
+289	Left_MI	L_MI_ROI
+290	Left_Pir	L_Pir_ROI
+291	Left_AVI	L_AVI_ROI
+292	Left_AAIC	L_AAIC_ROI
+293	Left_FOP1	L_FOP1_ROI
+294	Left_FOP3	L_FOP3_ROI
+295	Left_FOP2	L_FOP2_ROI
+296	Left_PFt	L_PFt_ROI
+297	Left_AIP	L_AIP_ROI
+298	Left_EC	L_EC_ROI
+299	Left_PreS	L_PreS_ROI
+300	Left_H	L_H_ROI
+301	Left_ProS	L_ProS_ROI
+302	Left_PeEc	L_PeEc_ROI
+303	Left_STGa	L_STGa_ROI
+304	Left_PBelt	L_PBelt_ROI
+305	Left_A5	L_A5_ROI
+306	Left_PHA1	L_PHA1_ROI
+307	Left_PHA3	L_PHA3_ROI
+308	Left_STSda	L_STSda_ROI
+309	Left_STSdp	L_STSdp_ROI
+310	Left_STSvp	L_STSvp_ROI
+311	Left_TGd	L_TGd_ROI
+312	Left_TE1a	L_TE1a_ROI
+313	Left_TE1p	L_TE1p_ROI
+314	Left_TE2a	L_TE2a_ROI
+315	Left_TF	L_TF_ROI
+316	Left_TE2p	L_TE2p_ROI
+317	Left_PHT	L_PHT_ROI
+318	Left_PH	L_PH_ROI
+319	Left_TPOJ1	L_TPOJ1_ROI
+320	Left_TPOJ2	L_TPOJ2_ROI
+321	Left_TPOJ3	L_TPOJ3_ROI
+322	Left_DVT	L_DVT_ROI
+323	Left_PGp	L_PGp_ROI
+324	Left_IP2	L_IP2_ROI
+325	Left_IP1	L_IP1_ROI
+326	Left_IP0	L_IP0_ROI
+327	Left_PFop	L_PFop_ROI
+328	Left_PF	L_PF_ROI
+329	Left_PFm	L_PFm_ROI
+330	Left_PGi	L_PGi_ROI
+331	Left_PGs	L_PGs_ROI
+332	Left_V6A	L_V6A_ROI
+333	Left_VMV1	L_VMV1_ROI
+334	Left_VMV3	L_VMV3_ROI
+335	Left_PHA2	L_PHA2_ROI
+336	Left_V4t	L_V4t_ROI
+337	Left_FST	L_FST_ROI
+338	Left_V3CD	L_V3CD_ROI
+339	Left_LO3	L_LO3_ROI
+340	Left_VMV2	L_VMV2_ROI
+341	Left_31pd	L_31pd_ROI
+342	Left_31a	L_31a_ROI
+343	Left_VVC	L_VVC_ROI
+344	Left_25	L_25_ROI
+345	Left_s32	L_s32_ROI
+346	Left_pOFC	L_pOFC_ROI
+347	Left_PoI1	L_PoI1_ROI
+348	Left_Ig	L_Ig_ROI
+349	Left_FOP5	L_FOP5_ROI
+350	Left_p10p	L_p10p_ROI
+351	Left_p47r	L_p47r_ROI
+352	Left_TGv	L_TGv_ROI
+353	Left_MBelt	L_MBelt_ROI
+354	Left_LBelt	L_LBelt_ROI
+355	Left_A4	L_A4_ROI
+356	Left_STSva	L_STSva_ROI
+357	Left_TE1m	L_TE1m_ROI
+358	Left_PI	L_PI_ROI
+359	Left_a32pr	L_a32pr_ROI
+360	Left_p24	L_p24_ROI