SCN pipeline – using custom atlas for DTI

[jonata...@gmail.com]

Hi Chris and everybody,

I'm trying to force skeletonised FA features (in accordance with the ICBM-81 White Matter atlas) to work in the structural covariance pipeline. 

After solving some issues, I've reached a point in where I cannot go any further – concretely, I cannot set the braingraph attributes to the adjacency matrices. Below the commands (and in yellow the error message):

> densities <- seq(0.05, 0.3, 0.01)

> corrs <- corr.matrix(all.dat.resids, densities = densities, what = 'resids')

> t(sapply(corrs, with, thresholds))                          

       [,1]      [,2]      [,3]      [,4]      [,5]      [,6]      [,7]      [,8]      [,9]     [,10]     [,11]

F 0.6553267 0.6446375 0.6337028 0.6209303 0.6058078 0.5990436 0.5939710 0.5843899 0.5755557 0.5671513 0.5655249

M 0.6547830 0.6352256 0.6258014 0.6169424 0.5956751 0.5927107 0.5878497 0.5785243 0.5728271 0.5697809 0.5668147

      [,12]     [,13]     [,14]     [,15]     [,16]     [,17]     [,18]     [,19]     [,20]     [,21]     [,22]

F 0.5577356 0.5508120 0.5475624 0.5407722 0.5314159 0.5302483 0.5225112 0.5187977 0.5181231 0.5136624 0.5100575

M 0.5588886 0.5551932 0.5476612 0.5432956 0.5355450 0.5320407 0.5264260 0.5176659 0.5136578 0.5083376 0.5054364

      [,23]     [,24]     [,25]     [,26]

F 0.5072010 0.5014536 0.4969798 0.4942124

M 0.5016274 0.4998780 0.4964702 0.4930049

> g <- lapply(corrs, function(x)

+   apply(x$r.thresh, 3,

+         graph_from_adjacency_matrix, 

+         mode = 'undirected', 

+         diag = F))

> g <- Map(function(x, y) 

+   plyr::llply(x, 

+               set_brainGraph_attr, 

+               atlas = atlas,                 

+               modality = 'thickness',

+               group = y, 

+               .progress = 'text'), 

+   g, as.list(groups))

Error in mapply(FUN = f, ..., SIMPLIFY = FALSE) : 

  zero-length inputs cannot be mixed with those of non-zero length

> traceback()

2: mapply(FUN = f, ..., SIMPLIFY = FALSE)

1: Map(function(x, y) plyr::llply(x, set_brainGraph_attr, atlas = atlas, 

       modality = "thickness", group = y, .progress = "text"), g, 

       as.list(groups))

Any thoughts on why this might be happening? Thanks in advance!

Best,

Jonatan

[Chris Watson]

Can you try with the latest version of brainGraph?

Chris

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[jonata...@gmail.com]

Hi Chris,

thanks for following. This is the new error w/brainGraph latest version:

> g <- lapply(seq_along(densities), function(x) 

               make_brainGraphList(corrs[x], modality = 'thickness'))

[1] "Start time: 2021-11-29 19:56:25"

  |                                                                                                           |   0%

 Error in { : task 1 failed - "object 'NA' not found" 

> traceback()

9: stop(simpleError(msg, call = expr))

8: e$fun(obj, substitute(ex), parent.frame(), e$data)

7: foreach(i = seq_len(kNumGraphs)) %dopar% {

       res <- loopfun(x[, , i], atlas, type, level, set.attrs, modality, 

           weighting, threshold[i], name = gnames[i], Group = grpNames[i], 

           subnet = subnet, mode = mode, diag = diag, weighted = weighted, 

           use.parallel = FALSE, ...)

   }

6: make_brainGraphList.array(A, atlas = atlas, type = type, level = level, 

       set.attrs = set.attrs, modality = modality, weighting = weighting, 

       threshold = threshold, mode = mode, weighted = weighted, 

       diag = diag, gnames = gnames, grpNames = grpNames, .progress = .progress, 

       ...)

5: make_brainGraphList(A, atlas = atlas, type = type, level = level, 

       set.attrs = set.attrs, modality = modality, weighting = weighting, 

       threshold = threshold, mode = mode, weighted = weighted, 

       diag = diag, gnames = gnames, grpNames = grpNames, .progress = .progress, 

       ...)

4: make_brainGraphList.corr_mats(corrs[x], modality = "thickness")

3: make_brainGraphList(corrs[x], modality = "thickness") at #1

2: FUN(X[[i]], ...)

1: lapply(seq_along(densities), function(x) make_brainGraphList(corrs[x], 

       modality = "thickness"))

[Chris Watson]

Could you first try with "set.attrs=F", to try to narrow down the error?

If there is nothing helpful there, I'll have to see the data and try to reproduce the error.

Chris

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[Chris Watson]

Thanks for sending the data.

There is a bug in "corr.matrix" when using a custom atlas. So you will have to add the following line *before* creating graphs:

corrs$atlas <- 'myAtlas'

where "myAtlas" would be replaced with the name of the atlas you are using. Then it should run without error.

Chris

[Chris Watson]

Actually you could also pass the "atlas" argument when calling "get.resid", and that should work as well.

Chris