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IBIC / neuropointillist

Flexible modeling of neuroimaging data in R
MIT License
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mask_4mm filename inconsistent #11

Open justbennet opened 5 years ago

justbennet commented 5 years ago

I believe you want to either modify these lines

./docs/fmri.example.md:cmdargs <- c("-m","mask_4mm.nii.gz", "--set1", "setfilenames1.txt",
./docs/fmri.example.md:These arguments specify a mask (`mask_4mm.nii.gz`), which has a value
./example.rawfmri/readargs.R:cmdargs <- c("-m","mask_4mm.nii.gz", "--set1", "setfilenames1.txt",

to not use the .gz extension or gzip the file example.rawfmri/mask_4mm.nii so that it is there. Currently, running npoint from example.rawfmri results in this warning.

$ npoint
Reading 2 data sets.
Allocating memory for data.
Reading in data.
    ++Working on dataset 1 
    ++Working on dataset 2 
           used  (Mb) gc trigger   (Mb)  max used   (Mb)
Ncells   328797  17.6     627465   33.6    627465   33.6
Vcells 74065756 565.1  168635876 1286.6 165340010 1261.5
no. of vertices 30546 
size 3054 
no. of jobs 10 
Warning message:
In normalizePath(args$mask) :
  path[1]="mask_4mm.nii.gz": No such file or directory