EOF in fscan

Managing anatomically complex model cells with the CellBuilder. Importing morphometric data with NEURON's Import3D tool or Robert Cannon's CVAPP. Where to find detailed morphometric data.
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alexandrapierri
Posts: 69
Joined: Wed Jun 17, 2015 5:31 pm

EOF in fscan

Post by alexandrapierri »

hello

I am using a L23 pyramidal neuron from the HBP cortical microcircuit, Aberra et al 2018 https://senselab.med.yale.edu/ModelDB/S ... del=241165. I replace the morphology of a L23 cortical cell with my own morphology, but I preserve mechnanisms and synapse distribution from the HBP. If the morphology is in neurolucida (asc) format I can load the cell succesfully and insert mechanisms and synapses. If instead the morphology is given in swc format, I can still load the cell successfully, insert mechanisms but I cannot insert synapses. I get the following error. I attach part of my swc file and part of the synapse file (tsv) from HBP. Any guidance on this error would help very much.

thank you,
Alexandra

Code: Select all

	1 
	1 
Starting to add synapses
/usr/local/lib/python3.9/site-packages/neuron/.data/bin//nrniv: EOF in fscan
 in init.hoc near line 49
 }
  ^
        Matrix[0].scanf(File[0])  // File[0] is the synapse file given in "tsv" format
      synapses_c2e79db05a[0].load_synapses(cADpyr229_L23_PC_c2e79db05a[0]) // cADpyr229_L23_PC_c2e79db05a is the swc morphology file
    cADpyr229_L23_PC_c2e79db05a[0].load_synapses()
  cADpyr229_L23_PC_c2e79db05a[0].init(1)
and others
here is part of my "swc" morpholgy file (not attached in full due to character limitations):

Code: Select all

1	1	308.512798	324.006748	61.7	0.15		-1
2	1	306.153	322.299	62	0.15		1
3	1	306.153	322.92	62	0.15		2
4	1	306.153	323.541	62	0.15		3
5	1	306.153	324.162	62	0.15		4
6	1	306.774	324.783	62	0.15		5
7	1	307.395	325.404	62	0.15		6
8	1	308.016	326.025	62	0.15		7
9	1	308.016	326.646	62	0.15		8
10	1	308.016	327.267	62	0.15		9
11	1	308.016	327.888	62	0.15		10
12	1	308.016	328.509	62	0.15		11
13	1	308.637	329.13	62	0.15		12
14	1	309.258	329.751	62	0.15		13
15	1	309.258	330.372	62	0.15		14
16	1	309.258	330.993	62	0.15		15
17	1	309.879	331.614	62	0.15		16
18	1	309.879	332.235	62	0.15		17
19	1	310.5	332.856	62	0.15		18
20	1	311.121	333.477	62	0.15		19
21	1	311.742	334.098	62	0.15		20
22	1	312.363	334.719	62	0.15		21
23	1	312.984	334.719	62	0.15		22
24	1	313.605	334.719	62	0.15		23
25	1	314.226	334.719	62	0.15		24
26	1	314.847	335.34	62	0.15		25
27	1	315.468	335.961	62	0.15		26
28	1	315.468	336.582	62	0.15		27
29	1	316.089	336.582	62	0.15		28
30	1	316.71	336.582	62	0.15		29
31	1	317.331	336.582	62	0.15		30
32	1	317.952	337.203	62	0.15		31
33	1	318.573	337.824	62	0.15		32
34	1	319.194	338.445	62	0.15		33
35	1	319.815	338.445	62	0.15		34
36	1	319.815	337.824	62	0.15		35
37	1	320.436	337.203	62	0.15		36
38	1	320.436	336.582	62	0.15		37
39	1	321.057	335.961	62	0.15		38
40	1	321.678	335.34	62	0.15		39
41	1	321.678	334.719	62	0.15		40
42	1	321.678	334.098	62	0.15		41
43	1	321.678	333.477	62	0.15		42
44	1	321.678	332.856	62	0.15		43
45	1	321.057	332.235	62	0.15		44
46	1	320.436	331.614	62	0.15		45
47	1	319.815	330.993	62	0.15		46
48	1	320.436	330.372	62	0.15		47
49	1	319.815	329.751	62	0.15		48
50	1	319.194	329.13	62	0.15		49
51	1	319.194	328.509	62	0.15		50
52	1	318.573	327.888	62	0.15		51
53	1	317.952	327.267	62	0.15		52
54	1	317.331	326.646	62	0.15		53
55	1	317.331	326.025	62	0.15		54
56	1	316.71	325.404	62	0.15		55
57	1	316.089	324.783	62	0.15		56
58	1	315.468	324.162	62	0.15		57
59	1	314.847	323.541	62	0.15		58
60	1	314.226	323.541	62	0.15		59
61	1	313.605	322.92	62	0.15		60
62	1	312.984	322.92	62	0.15		61
63	1	312.363	322.92	62	0.15		62
64	1	311.742	322.299	62	0.15		63
65	1	311.121	321.678	62	0.15		64
66	1	310.5	321.057	62	0.15		65
67	1	309.879	321.678	62	0.15		66
68	1	309.258	321.057	62	0.15		67
69	1	308.637	321.057	62	0.15		68
70	1	308.016	320.436	62	0.15		69
71	1	307.395	320.436	62	0.15		70
72	1	306.774	320.436	62	0.15		71
73	1	306.774	321.057	62	0.15		72
74	1	306.153	321.678	62	0.15		73
75	1	306.153	322.299	62	0.15		74
76	1	306.153	322.92	62	0.15		75
77	3	310.872596	325.714496	61.4	0.15		1
78	4	307.394996	321.677996	60	0.15		77
79	4	306.773996	321.056996	60	0.15		78
80	4	306.152996	320.435996	60	0.15		79
81	4	305.531996	319.814996	60	0.15		80
82	4	304.910996	319.193996	60	0.15		81
83	4	304.289996	318.572996	60	0.15		82
84	4	303.668996	317.951996	60	0.15		83
85	4	303.047996	317.330996	60	0.15		84
86	4	302.426996	316.709996	60	0.15		85
87	4	302.426996	316.088996	60	0.15		86
88	4	301.805996	315.467996	60	0.15		87
89	4	301.184996	314.846996	60	0.15		88
90	4	300.563996	314.225996	60	0.15		89
91	4	299.942996	313.604996	60	0.15		90
92	4	299.321996	312.983996	60	0.15		91
93	4	299.321996	312.362996	60	0.15		92
94	4	298.700996	311.741996	60	0.15		93
95	4	298.700996	311.120996	60	0.15		94
96	4	298.079996	310.499996	58	0.15		95
97	4	298.079996	309.878996	56	0.15		96
98	4	298.079996	309.257996	56	0.15		97
99	4	297.458996	308.636996	56	0.15		98
100	4	296.837996	308.015996	56	0.15		99
101	4	296.216996	307.394996	56	0.15		100
102	4	295.595996	306.773996	56	0.15		101
103	4	294.974996	306.152996	56	0.15		102
104	4	294.974996	305.531996	56	0.15		103
105	4	294.353996	304.910996	56	0.15		104
106	4	293.732996	304.289996	56	0.15		105
107	4	293.111996	303.668996	56	0.15		106
108	4	292.490996	303.047996	56	0.15		107
109	4	292.490996	302.426996	56	0.15		108
110	4	291.869996	301.805996	56	0.15		109
111	4	291.248996	301.184996	56	0.15		110
112	4	290.627996	300.563996	56	0.15		111
113	4	290.006996	299.942996	56	0.15		112
114	4	289.385996	299.321996	56	0.15		113
115	4	288.764996	298.700996	56	0.15		114
116	4	288.143996	298.079996	56	0.15		115
117	4	287.522996	297.458996	56	0.15		116
118	4	286.901996	296.837996	56	0.15		117
119	4	286.280996	296.216996	56	0.15		118
120	4	285.659996	295.595996	56	0.15		119
121	4	285.038996	294.974996	56	0.15		120
122	4	284.417996	294.353996	56	0.15		121
123	4	283.796996	293.732996	56	0.15		122
124	4	283.175996	293.111996	56	0.15		123
125	4	282.554996	292.490996	56	0.15		124
126	4	281.933996	291.869996	56	0.15		125
127	4	281.312996	291.248996	56	0.15		126
128	4	281.312996	290.627996	56	0.15		127
129	4	280.691996	290.006996	56	0.15		128
130	4	280.070996	289.385996	56	0.15		129
131	4	279.449996	288.764996	56	0.15		130
132	4	278.828996	288.143996	56	0.15		131
133	4	278.207996	287.522996	56	0.15		132
134	4	277.586996	286.901996	56	0.15		133
135	4	276.965996	286.280996	56	0.15		134
136	4	276.965996	285.659996	56	0.15		135
137	4	276.344996	285.038996	56	0.15		136
138	4	275.723996	284.417996	56	0.15		137
139	4	275.102996	283.796996	56	0.15		138
140	4	275.102996	283.175996	56	0.15		139
141	4	274.481996	282.554996	56	0.15		140
142	4	273.860996	281.933996	56	0.15		141
143	4	273.239996	281.312996	56	0.15		142
144	4	272.618996	280.691996	56	0.15		143
145	4	271.997996	280.070996	56	0.15		144
146	4	271.376996	279.449996	56	0.15		145
147	4	270.755996	278.828996	56	0.15		146
148	4	270.134996	278.207996	56	0.15		147
149	4	269.513996	278.207996	56	0.15		148
150	4	268.892996	277.586996	56	0.15		149
151	4	268.271996	276.965996	56	0.15		150
152	4	267.650997	276.965996	56	0.15		151
153	4	267.029997	276.344996	54	0.15		152
154	4	266.408997	275.723996	52	0.15		153
155	4	265.787997	275.102996	52	0.15		154
156	4	265.166997	274.481996	52	0.15		155
157	4	264.545997	273.860996	52	0.15		156
158	4	264.545997	273.239996	52	0.15		157
159	4	264.545997	272.618996	52	0.15		158
160	4	264.545997	271.997996	52	0.15		159
161	4	263.924997	271.376996	52	0.15		160
162	4	263.924997	270.755996	52	0.15		161
163	4	263.924997	270.134996	50	0.15		162
164	4	263.303997	269.513996	50	0.15		163
165	4	263.303997	268.892996	50	0.15		164
166	4	262.682997	268.271996	50	0.15		165
167	4	262.682997	267.650997	50	0.15		166
168	4	262.061997	267.029997	50	0.15		167
169	4	262.061997	266.408997	50	0.15		168
170	4	262.061997	265.787997	50	0.15		169
171	4	262.061997	265.166997	50	0.15		170
172	4	261.440997	264.545997	50	0.15		171
173	4	261.440997	263.924997	50	0.15		172
174	4	260.819997	263.303997	50	0.15		173
175	4	260.819997	262.682997	50	0.15		174
176	4	260.198997	262.061997	50	0.15		175
177	4	260.198997	261.440997	50	0.15		176
178	4	259.577997	260.819997	50	0.15		177
179	4	258.956997	260.198997	50	0.15		178
180	4	258.956997	259.577997	50	0.15		179
181	4	258.956997	258.956997	50	0.15		180
182	4	258.956997	258.335997	50	0.15		181
183	4	258.956997	257.714997	50	0.15		182
184	4	258.335997	257.093997	50	0.15		183
185	4	258.335997	256.472997	50	0.15		184
186	4	258.335997	255.851997	50	0.15		185
187	4	257.714997	255.230997	50	0.15		186
188	4	257.714997	254.609997	50	0.15		187
189	4	257.093997	253.988997	50	0.15		188
190	4	257.093997	253.367997	50	0.15		189
191	4	257.093997	252.746997	50	0.15		190
192	4	256.472997	252.125997	50	0.15		191
193	4	255.851997	251.504997	50	0.15		192
194	4	255.851997	250.883997	50	0.15		193
195	4	255.230997	250.262997	50	0.15		194
196	4	254.609997	249.641997	50	0.15		195
197	4	254.609997	249.020997	50	0.15		196
198	4	253.988997	248.399997	48	0.15		197
199	4	253.367997	247.778997	46	0.15		198
200	4	253.367997	247.157997	46	0.15		199
201	4	253.367997	246.536997	46	0.15		200
202	4	252.746997	245.915997	46	0.15		201
203	4	252.125997	245.294997	46	0.15		202
204	4	251.504997	244.673997	46	0.15		203
205	4	250.883997	244.052997	46	0.15		204
206	4	250.883997	243.431997	46	0.15		205
207	4	250.262997	242.810997	44	0.15		206
208	4	249.641997	242.189997	44	0.15		207
209	4	249.641997	241.568997	44	0.15		208
210	4	249.641997	240.947997	44	0.15		209
211	4	249.020997	240.326997	44	0.15		210
212	4	248.399997	239.705997	44	0.15		211
213	4	247.778997	239.084997	44	0.15		212
214	4	247.157997	238.463997	44	0.15		213
215	4	246.536997	237.842997	44	0.15		214
216	4	245.915997	237.221997	44	0.15		215
217	4	245.294997	236.600997	44	0.15		216
218	4	244.673997	235.979997	44	0.15		217
219	4	244.052997	235.979997	42	0.15		218
220	4	243.431997	235.358997	42	0.15		219
221	4	242.810997	234.737997	42	0.15		220
222	4	242.189997	234.116997	42	0.15		221
223	4	241.568997	233.495997	42	0.15		222
224	4	240.947997	232.874997	42	0.15		223
225	4	240.326997	232.253997	42	0.15		224
226	4	239.705997	231.632997	42	0.15		225
227	4	239.084997	231.011997	42	0.15		226
228	4	238.463997	230.390997	42	0.15		227
229	4	237.842997	229.769997	42	0.15		228
230	4	237.221997	229.148997	42	0.15		229
231	4	237.221997	228.527997	42	0.15		230
232	4	237.221997	227.906997	42	0.15		231
233	4	236.600997	227.285997	42	0.15		232
234	4	235.979997	226.664997	42	0.15		233
235	4	235.358997	226.043997	42	0.15		234

here is a section of my "tsv" synapse file (not attached in full due to character limitations):

Code: Select all

2016 13
0       94      3       2       6       0.211   1       357     13      0.138080761     6.405982018     0.845154        0.355495542
1       94      3       2       6       0.285   1       1013    28      0.348402381     9.965270996     0.865298        1.245317817
2       94      3       2       7       0.44    1       464     16      0.172165632     6.982802868     0.810012        0.499700785
3       94      3       2       6       0.66    1       974     27      0.336079419     9.756729126     1.08069 1.193182111
4       94      3       2       6       0.691   1       705     21      0.249655113     8.294163704     1.0901  0.827540874
5       94      3       2       6       0.687   1       400     14      0.151754469     6.637383461     1.08819 0.413345844
6       94      3       2       2       0.744   1       1059    29      0.363257229     10.2166605      0.278215        1.308165193
7       94      3       2       5       0.932   1       810     23      0.28342405      8.865637779     0.62132 0.970409393
8       94      3       2       15      0.52    1       496     16      0.182497784     7.157654762     0.879054        0.543413758
9       94      3       2       15      0.375   1       900     25      0.312317193     9.354598045     0.860576        1.092649579
10      299     1       2       5       0.315   1       682     20      0.242313921     8.169927597     0.334955        0.796481967
11      299     1       2       5       0.872   1       412     14      0.155746862     6.704946995     0.458591        0.430236697
12      299     1       2       5       0.904   1       1050    29      0.360547423     10.17080307     0.420983        1.296700716
13      299     1       2       5       0.935   1       735     22      0.259467244     8.460215569     0.438052        0.869053781
14      299     1       2       5       0.966   1       356     13      0.137626112     6.39828825      0.455293        0.353572011
15      299     1       2       5       0.547   1       352     13      0.136258483     6.375143528     0.778867        0.34778589
16      299     1       2       5       0.561   1       879     25      0.305625737     9.241358757     0.802841        1.064339638
17      299     1       2       5       0.749   1       1007    28      0.346540362     9.933759689     0.91105 1.23743999
18      299     1       2       5       0.788   1       1053    29      0.361379147     10.1848774      0.930229        1.300219417
19      299     1       2       5       0.791   1       1036    28      0.355896086     10.09208775     0.931446        1.277022004
20      299     1       2       5       0.836   1       352     13      0.136416897     6.377824306     0.952782        0.348456115
21      299     1       2       12      0.481   1       997     27      0.343250483     9.878085136     0.830943        1.223521233
22      620     6       1       5       0.467   119     673     17      0.48305437      1.755960703     1.04076 0.724788487
23      620     6       1       5       0.461   119     662     14      0.328911752     1.649246573     1.04936 0.452074647
ted
Site Admin
Posts: 6317
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: EOF in fscan

Post by ted »

Something is broken--maybe the file that is being fscanned. Does your code work with some other data file?

Can't say more without being able to reproduce the problem myself.
alexandrapierri
Posts: 69
Joined: Wed Jun 17, 2015 5:31 pm

Re: EOF in fscan

Post by alexandrapierri »

yes the file being scanned was corrupted. I fixed it, thank you!
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