AFNI
DataTable
3dMVM
and 3dLME
can take an input table like 3dMVM … -dataTable @myfile.tsv
. Both are very particular about the format of the input file.
Subj
must be the name of the first column (and thus the first word of the file)InputFile
must also exist and be a valid 3D file. You will get an error if any row has an inputfile that is more than one volume (4D; file with many “briks”;3dinfo -nt
> 1) and does not have a sub-brik specifier ( ❌deconve_output.nii.gz
; ✅deconv_output.nii.gz[Coef#0]
)
Building
Here's example GNU R code to add InputFile
to an existing dataframe df
1)
path_prefix <- '/Volumes/Hera/Datasets/adept/data/tat2/sub-' df <- df %>% mutate(InputFile = paste0(path_prefix, subjid, '_ses-0', visit, '_tat2.nii.gz')) %>% filter(file.exists(InputFile))
Other Tools
4dConcatDataTable
(an lncdtool) reuses the same dataTable format to create 4D images useful for the “graph” view in AFNI's GUI.maskvolume
uses 3dROIstats w/mask as input and mask to get ROI sizes in mm^33dmaskave_grp
uses 3dmaskave or 3dROIstats to get roi averages in parallel to a single file
Backlinks
1)
from Finn circa 2023-09