ADNI4 visits?

Ramiro Magno

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Apr 22, 2025, 2:27:29 PMApr 22

to Alzheimer's Disease Neuroimaging Initiative (ADNI) Data

Is the VISITS data set supposed to include ADNI4 visits?

This is data from 12 Mar 2025.

> visits() |> print(n = Inf)

# A tibble: 59 × 5
PHASE ID VISCODE VISNAME VISORDER
<chr> <int> <chr> <chr> <int>
1 ADNI1 1 sc Screening 1
2 ADNI1 2 bl Baseline 2
3 ADNI1 3 m06 Month 6 3
4 ADNI1 4 m12 Month 12 4
5 ADNI1 5 m18 Month 18 5
6 ADNI1 6 m24 Month 24 6
7 ADNI1 7 m30 Month 30 7
8 ADNI1 8 m36 Month 36 8
9 ADNI1 9 m42 Month 42 9
10 ADNI1 10 m48 Month 48 10
11 ADNI1 11 m54 Month 54 11
12 ADNI1 12 uns1 Unscheduled NA
13 ADNI1 13 f Screen Fail NA
14 ADNI1 14 nv No Visit Defined NA
15 ADNIGO 1 sc Screening 1
16 ADNIGO 2 scmri Screening MRI 2
17 ADNIGO 3 bl Baseline 3
18 ADNIGO 4 m03 Month 3 MRI 4
19 ADNIGO 5 m06 Month 6 5
20 ADNIGO 6 m12 Month 12 6
21 ADNIGO 7 m18 Month 18 7
22 ADNIGO 8 m36 Month 36 8
23 ADNIGO 9 m42 Month 42 9
24 ADNIGO 10 m48 Month 48 10
25 ADNIGO 11 m54 Month 54 11
26 ADNIGO 12 m60 Month 60 12
27 ADNIGO 13 m66 Month 66 13
28 ADNIGO 14 m72 Month 72 14
29 ADNIGO 15 m78 Month 78 15
30 ADNIGO 16 nv No Visit Defined NA
31 ADNI2 1 v01 Screening - New Pt 1
32 ADNI2 2 v02 Screening MRI - New Pt 2
33 ADNI2 3 v03 Baseline - New Pt 3
34 ADNI2 4 v04 Month 3 MRI - New Pt 4
35 ADNI2 5 v05 Month 6 - New Pt 5
36 ADNI2 6 v06 ADNI2 Initial Visit - Continuing Pt 6
37 ADNI2 7 v07 ADNI2 Initial TelCheck - Continuing Pt 7
38 ADNI2 8 v11 ADNI2 Year 1 Visit 8
39 ADNI2 9 v12 ADNI2 Year 1 TelCheck 9
40 ADNI2 10 v21 ADNI2 Year 2 Visit 10
41 ADNI2 11 v22 ADNI2 Year 2 TelCheck 11
42 ADNI2 12 v31 ADNI2 Year 3 Visit 12
43 ADNI2 13 v32 ADNI2 Year 3 TelCheck 13
44 ADNI2 14 v41 ADNI2 Year 4 Visit 14
45 ADNI2 15 v42 ADNI2 Year 4 TelCheck 15
46 ADNI2 16 v51 ADNI2 Year 5 Visit 16
47 ADNI2 17 v52 ADNI2 Year 5 TelCheck 17
48 ADNI2 18 nv No Visit Defined NA
49 ADNI2 19 tau ADNI2 Tau-only visit NA
50 ADNI3 1 reg Participant Registration 1
51 ADNI3 2 sc Screening - New Pt 2
52 ADNI3 3 bl Baseline - New Pt 3
53 ADNI3 4 init ADNI3 Initial Visit - Continuing Pt 4
54 ADNI3 5 y1 ADNI3 Year 1 Visit 5
55 ADNI3 6 y2 ADNI3 Year 2 Visit 6
56 ADNI3 7 y3 ADNI3 Year 3 Visit 7
57 ADNI3 8 y4 ADNI3 Year 4 Visit 8
58 ADNI3 9 y5 ADNI3 Year 5 Visit 9
59 ADNI3 10 y6 ADNI3 Year 6 Visit 10

Ramiro Magno

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Apr 22, 2025, 2:33:43 PMApr 22

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From the REGISTRY I get these many more PHASE-VISCODE2 combinations:

library(adni.clinical)
registry() |>
dplyr::count(PHASE, VISCODE2) |>
dplyr::mutate(PHASE = factor(PHASE, levels = enum_adni_phases())) |>
dplyr::arrange(PHASE) |>
print(n = Inf)
#> # A tibble: 123 × 3
#> PHASE VISCODE2 n
#> <fct> <chr> <int>
#> 1 ADNI1 bl 822
#> 2 ADNI1 f 564
#> 3 ADNI1 m06 819
#> 4 ADNI1 m12 818
#> 5 ADNI1 m18 813
#> 6 ADNI1 m24 797
#> 7 ADNI1 m30 661
#> 8 ADNI1 m36 619
#> 9 ADNI1 m42 414
#> 10 ADNI1 m48 248
#> 11 ADNI1 m54 137
#> 12 ADNI1 sc 822
#> 13 ADNI1 uns1 1
#> 14 ADNIGO bl 136
#> 15 ADNIGO m03 125
#> 16 ADNIGO m06 121
#> 17 ADNIGO m12 31
#> 18 ADNIGO m18 15
#> 19 ADNIGO m36 9
#> 20 ADNIGO m42 9
#> 21 ADNIGO m48 147
#> 22 ADNIGO m54 137
#> 23 ADNIGO m60 92
#> 24 ADNIGO m66 67
#> 25 ADNIGO m72 6
#> 26 ADNIGO m78 5
#> 27 ADNIGO sc 616
#> 28 ADNIGO scmri 153
#> 29 ADNI2 bl 804
#> 30 ADNI2 m03 769
#> 31 ADNI2 m06 765
#> 32 ADNI2 m102 192
#> 33 ADNI2 m108 184
#> 34 ADNI2 m114 114
#> 35 ADNI2 m12 863
#> 36 ADNI2 m120 99
#> 37 ADNI2 m126 28
#> 38 ADNI2 m132 6
#> 39 ADNI2 m138 2
#> 40 ADNI2 m18 824
#> 41 ADNI2 m24 796
#> 42 ADNI2 m30 656
#> 43 ADNI2 m36 623
#> 44 ADNI2 m42 531
#> 45 ADNI2 m48 503
#> 46 ADNI2 m54 230
#> 47 ADNI2 m60 349
#> 48 ADNI2 m66 229
#> 49 ADNI2 m72 282
#> 50 ADNI2 m78 258
#> 51 ADNI2 m84 242
#> 52 ADNI2 m90 222
#> 53 ADNI2 m96 218
#> 54 ADNI2 sc 1289
#> 55 ADNI2 scmri 890
#> 56 ADNI2 <NA> 41
#> 57 ADNI3 bl 695
#> 58 ADNI3 m102 95
#> 59 ADNI3 m108 98
#> 60 ADNI3 m114 68
#> 61 ADNI3 m12 490
#> 62 ADNI3 m120 81
#> 63 ADNI3 m126 60
#> 64 ADNI3 m132 88
#> 65 ADNI3 m138 39
#> 66 ADNI3 m144 54
#> 67 ADNI3 m150 25
#> 68 ADNI3 m156 33
#> 69 ADNI3 m162 23
#> 70 ADNI3 m168 29
#> 71 ADNI3 m174 13
#> 72 ADNI3 m18 29
#> 73 ADNI3 m180 27
#> 74 ADNI3 m186 15
#> 75 ADNI3 m192 13
#> 76 ADNI3 m198 8
#> 77 ADNI3 m204 3
#> 78 ADNI3 m24 278
#> 79 ADNI3 m30 66
#> 80 ADNI3 m36 224
#> 81 ADNI3 m42 51
#> 82 ADNI3 m48 185
#> 83 ADNI3 m54 65
#> 84 ADNI3 m60 114
#> 85 ADNI3 m66 113
#> 86 ADNI3 m72 131
#> 87 ADNI3 m78 128
#> 88 ADNI3 m84 128
#> 89 ADNI3 m90 120
#> 90 ADNI3 m96 112
#> 91 ADNI3 sc 1102
#> 92 ADNI3 <NA> 369
#> 93 ADNI4 bl 281
#> 94 ADNI4 m12 30
#> 95 ADNI4 m126 2
#> 96 ADNI4 m132 16
#> 97 ADNI4 m138 18
#> 98 ADNI4 m144 21
#> 99 ADNI4 m150 22
#> 100 ADNI4 m156 28
#> 101 ADNI4 m162 8
#> 102 ADNI4 m168 4
#> 103 ADNI4 m18 5
#> 104 ADNI4 m204 3
#> 105 ADNI4 m210 4
#> 106 ADNI4 m216 7
#> 107 ADNI4 m222 6
#> 108 ADNI4 m228 2
#> 109 ADNI4 m24 23
#> 110 ADNI4 m30 21
#> 111 ADNI4 m36 40
#> 112 ADNI4 m42 15
#> 113 ADNI4 m48 9
#> 114 ADNI4 m54 16
#> 115 ADNI4 m60 33
#> 116 ADNI4 m66 38
#> 117 ADNI4 m72 88
#> 118 ADNI4 m78 55
#> 119 ADNI4 m84 24
#> 120 ADNI4 m90 4
#> 121 ADNI4 m96 1
#> 122 ADNI4 sc 562
#> 123 ADNI4 <NA> 7

Danielle J Harvey

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Apr 22, 2025, 2:38:55 PMApr 22

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Hi Ramiro,

VISCODE2 is not the same as VISCODE (though the ADNIMERGE file uses VISCODE in place of VISCODE2). The VISITS table gave a list of visits one might expect for the different phases of ADNI along with the tracking visit code (VISCODE)…that tracking VISCODE wasn’t always meaningful, so VISCODE2 was created to be a bit more interpretable by the user. I don’t know if the Clinical Core will add the expected visits to the VISITS table…

Danielle

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Ramiro Magno

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Apr 22, 2025, 2:50:21 PMApr 22

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Hi Danielle,

Thanks for the quick response.

I think I got the difference between VISCODE and VISCODE2.

I'm not referring to expected visits but visits that already took place, as can be seen, they show up in the registry.

How can I access all valid visits, i.e. PHASE / VISCODE2 combinations? I thought VISITS provided that but it's not complete, as it misses ADNI4 (at least).

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Danielle J Harvey

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Apr 22, 2025, 4:59:39 PMApr 22

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Hi Ramiro,

I usually think of REGISTRY as giving the complete list of visits that occurred (I believe there is a variable that indicates whether the visit happened or not, so you will want to filter on that). That being said, imaging and blood draws may not occur at the same time as the clinical visit (and the clinical visit may happen over a few days), so dates of visits/scans/blood may not all align.

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Ramiro Magno

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Apr 22, 2025, 5:25:38 PMApr 22

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Thanks Danielle.

I think my mental model of these datasets might be wrong.

I'm trying to create an ordered factor for VISCODE2 that spans all PHASEs.

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Danielle J Harvey

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Apr 22, 2025, 5:40:34 PMApr 22

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Hi Ramiro,

At one point, VISCODE2 mapped the VISCODE to the visit (generally in terms of months since baseline…so the VISCODE representing the m24 visit would get m24). I believe more recently, VISCODE2 has been updated to be in 6 month intervals, using the dates of the initial visit and the current visit and then rounding to the closest half-year/year(s). So, other than sc, scmri, bl, f, and uns1, the number following “m” in VISCODE2 will represent the months since baseline rounded to the nearest 6 months. “sc” and “scmri” are for the screening visit and screening MRI (so they happen first). “bl” is for the baseline visit and would come next. Some information is collected as the screening visit and then additional information is collected at the baseline visit, if someone passes screening…so you will find “initial” information in both “sc” and “bl”. “f” represents someone failing screening, so they didn’t actually end up enrolling in the study. “uns1”, I believe was used in ADNI1 to refer to “visits” that didn’t seem to correspond to a known visit.

Does that help?

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Ramiro Magno

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Apr 22, 2025, 6:01:25 PMApr 22

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Yes, definitely! Thank you for your patience.

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Ramiro Magno

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Apr 22, 2025, 6:26:23 PMApr 22

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So I guess that if I want a global VISCODE to sort longitudinal datasets, this viscode3 of mine would be it, right?

# A tibble: 118 × 3
    PHASE  VISCODE2 viscode3      
    <chr>  <chr>    <chr>         
  1 ADNI1  sc       ADNI1 - sc    
  2 ADNI1  bl       ADNI1 - bl    
  3 ADNI1  m06      ADNI1 - 006   
  4 ADNI1  m12      ADNI1 - 012   
  5 ADNI1  m18      ADNI1 - 018   
  6 ADNI1  m24      ADNI1 - 024   
  7 ADNI1  m30      ADNI1 - 030   
  8 ADNI1  m36      ADNI1 - 036   
  9 ADNI1  m42      ADNI1 - 042   
 10 ADNI1  m48      ADNI1 - 048   
 11 ADNI1  m54      ADNI1 - 054   
 12 ADNIGO sc       ADNIGO - sc   
 13 ADNIGO scmri    ADNIGO - scmri
 14 ADNIGO bl       ADNIGO - bl   
 15 ADNIGO m03      ADNIGO - 003  
 16 ADNIGO m06      ADNIGO - 006  
 17 ADNIGO m12      ADNIGO - 012  
 18 ADNIGO m18      ADNIGO - 018  
 19 ADNIGO m36      ADNIGO - 036  
 20 ADNIGO m42      ADNIGO - 042  
 21 ADNIGO m48      ADNIGO - 048  
 22 ADNIGO m54      ADNIGO - 054  
 23 ADNIGO m60      ADNIGO - 060  
 24 ADNIGO m66      ADNIGO - 066  
 25 ADNIGO m72      ADNIGO - 072  
 26 ADNIGO m78      ADNIGO - 078  
 27 ADNI2  sc       ADNI2 - sc    
 28 ADNI2  scmri    ADNI2 - scmri 
 29 ADNI2  bl       ADNI2 - bl    
 30 ADNI2  m03      ADNI2 - 003   
 31 ADNI2  m06      ADNI2 - 006   
 32 ADNI2  m12      ADNI2 - 012   
 33 ADNI2  m18      ADNI2 - 018   
 34 ADNI2  m24      ADNI2 - 024   
 35 ADNI2  m30      ADNI2 - 030   
 36 ADNI2  m36      ADNI2 - 036   
 37 ADNI2  m42      ADNI2 - 042   
 38 ADNI2  m48      ADNI2 - 048   
 39 ADNI2  m54      ADNI2 - 054   
 40 ADNI2  m60      ADNI2 - 060   
 41 ADNI2  m66      ADNI2 - 066   
 42 ADNI2  m72      ADNI2 - 072   
 43 ADNI2  m78      ADNI2 - 078   
 44 ADNI2  m84      ADNI2 - 084   
 45 ADNI2  m90      ADNI2 - 090   
 46 ADNI2  m96      ADNI2 - 096   
 47 ADNI2  m102     ADNI2 - 102   
 48 ADNI2  m108     ADNI2 - 108   
 49 ADNI2  m114     ADNI2 - 114   
 50 ADNI2  m120     ADNI2 - 120   
 51 ADNI2  m126     ADNI2 - 126   
 52 ADNI2  m132     ADNI2 - 132   
 53 ADNI2  m138     ADNI2 - 138   
 54 ADNI3  sc       ADNI3 - sc    
 55 ADNI3  bl       ADNI3 - bl    
 56 ADNI3  m12      ADNI3 - 012   
 57 ADNI3  m18      ADNI3 - 018   
 58 ADNI3  m24      ADNI3 - 024   
 59 ADNI3  m30      ADNI3 - 030   
 60 ADNI3  m36      ADNI3 - 036   
 61 ADNI3  m42      ADNI3 - 042   
 62 ADNI3  m48      ADNI3 - 048   
 63 ADNI3  m54      ADNI3 - 054   
 64 ADNI3  m60      ADNI3 - 060   
 65 ADNI3  m66      ADNI3 - 066   
 66 ADNI3  m72      ADNI3 - 072   
 67 ADNI3  m78      ADNI3 - 078   
 68 ADNI3  m84      ADNI3 - 084   
 69 ADNI3  m90      ADNI3 - 090   
 70 ADNI3  m96      ADNI3 - 096   
 71 ADNI3  m102     ADNI3 - 102   
 72 ADNI3  m108     ADNI3 - 108   
 73 ADNI3  m114     ADNI3 - 114   
 74 ADNI3  m120     ADNI3 - 120   
 75 ADNI3  m126     ADNI3 - 126   
 76 ADNI3  m132     ADNI3 - 132   
 77 ADNI3  m138     ADNI3 - 138   
 78 ADNI3  m144     ADNI3 - 144   
 79 ADNI3  m150     ADNI3 - 150   
 80 ADNI3  m156     ADNI3 - 156   
 81 ADNI3  m162     ADNI3 - 162   
 82 ADNI3  m168     ADNI3 - 168   
 83 ADNI3  m174     ADNI3 - 174   
 84 ADNI3  m180     ADNI3 - 180   
 85 ADNI3  m186     ADNI3 - 186   
 86 ADNI3  m192     ADNI3 - 192   
 87 ADNI3  m198     ADNI3 - 198   
 88 ADNI3  m204     ADNI3 - 204   
 89 ADNI4  sc       ADNI4 - sc    
 90 ADNI4  bl       ADNI4 - bl    
 91 ADNI4  m12      ADNI4 - 012   
 92 ADNI4  m18      ADNI4 - 018   
 93 ADNI4  m24      ADNI4 - 024   
 94 ADNI4  m30      ADNI4 - 030   
 95 ADNI4  m36      ADNI4 - 036   
 96 ADNI4  m42      ADNI4 - 042   
 97 ADNI4  m48      ADNI4 - 048   
 98 ADNI4  m54      ADNI4 - 054   
 99 ADNI4  m60      ADNI4 - 060   
100 ADNI4  m66      ADNI4 - 066   
101 ADNI4  m72      ADNI4 - 072   
102 ADNI4  m78      ADNI4 - 078   
103 ADNI4  m84      ADNI4 - 084   
104 ADNI4  m90      ADNI4 - 090   
105 ADNI4  m96      ADNI4 - 096   
106 ADNI4  m126     ADNI4 - 126   
107 ADNI4  m132     ADNI4 - 132   
108 ADNI4  m138     ADNI4 - 138   
109 ADNI4  m144     ADNI4 - 144   
110 ADNI4  m150     ADNI4 - 150   
111 ADNI4  m156     ADNI4 - 156   
112 ADNI4  m162     ADNI4 - 162   
113 ADNI4  m168     ADNI4 - 168   
114 ADNI4  m204     ADNI4 - 204   
115 ADNI4  m210     ADNI4 - 210   
116 ADNI4  m216     ADNI4 - 216   
117 ADNI4  m222     ADNI4 - 222   
118 ADNI4  m228     ADNI4 - 228

Danielle J Harvey

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Apr 22, 2025, 6:47:18 PMApr 22

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Hi Ramiro,

It might be a little bit more complex than that, since we have “roll-overs” from one phase to another phase in ADNI, so their “months” don’t restart at the next phase. For example, someone might go from ADNI-1 m36 to ADNI-GO m60 (if they also missed some visits). What are you trying to do with this list of visits?

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Ramiro Magno

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Apr 22, 2025, 6:59:18 PMApr 22

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Oh... are the levels of VISCODE2 (e.g., "m06", "m12", etc.) already global across phases? However, values like "sc", "scmri", and "bl" seem to be local to each PHASE, right?

What I'm looking for is a globally ordered factor of visits that excludes records that are not actual visits — such as "uns1" or "f". Essentially, given a long-format longitudinal dataset, I want to create a new ordered factor variable that correctly arranges all realized visits across the full study timeline.

It seems that VISCODE2 almost does the job, except for the values like "sc", "scmri", and "bl", which are phase-specific and therefore not globally comparable.

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Danielle J Harvey

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Apr 22, 2025, 7:05:10 PMApr 22

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Hi Ramiro,

Within participant, VISCODE2 should already be in order (other than making sc, scmri and bl come first) across phases. That said, we often encourage researchers to use the EXAMDATE variable (and EXAMDATE from bl or sc visit) to get the actual time since the initial visit.

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Ramiro Magno

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Apr 22, 2025, 7:31:57 PMApr 22

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Hi Danielle,

Thank you for bearing with me — I was really making a mess of it!

I now understand that VISCODE2 is exactly what I need. I’ll also make use of EXAMDATE from either bl or sc.

These are the helpers I'm adding to my code:

#' VISCODE2 codes
#'
#' [viscode2_codes()] returns a fixed, standardized character vector of ADNI
#' `VISCODE2` visit labels. It includes early visits such as `"sc"` and `"bl"`,
#' as well as month-based follow-up visits (e.g., `"m03"`, `"m06"`, ..., `"m228"`),
#' ordered chronologically.
#'
#' This function is used to define a consistent factor level ordering for visit codes
#' across ADNI phases and datasets.
#'
#' @returns
#' A character vector of visit codes:
#' \itemize{
#' \item `"sc"`, `"scmri"`: screening visits
#' \item `"bl"`: baseline
#' \item `"m03"`, `"m06"`, ..., `"m228"`: follow-up months
#' }
#'
#' @examples
#' viscode2_codes()
#'
#' @export
viscode2_codes <- function() {
c(
"sc", "scmri", "bl",
"m03", "m06", "m12", "m18", "m24", "m30", "m36", "m42", "m48", "m54", "m60", "m66",
"m72", "m78", "m84", "m90", "m96", "m102", "m108", "m114", "m120", "m126", "m132",
"m138", "m144", "m150", "m156", "m162", "m168", "m174", "m180", "m186", "m192",
"m198", "m204", "m210", "m216", "m222", "m228"
)
}

#' Convert VISCODE2 to factor
#'
#' [as_viscode2_fct()] converts a character vector of ADNI `VISCODE2` visit labels
#' into an ordered factor using a standardized level set, so that visits are arranged
#' chronologically for plotting or modeling purposes.
#'
#' Visit codes not present in the level set will be returned as `NA`.
#'
#' @param viscode2 A character vector of visit codes (e.g., `"bl"`, `"m06"`, `"m12"`).
#'
#' @returns
#' An factor with chronological levels defined by [viscode2_codes()].
#'
#' @examples
#' as_viscode2_fct(c("bl", "m06", "m12", "sc", "m03"))
#'
#' @export
as_viscode2_fct <- function(viscode2) {
factor(viscode2, levels = viscode2_codes())
}

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