NITRC ciftiTools: Tools for Reading, Writing, Viewing and Manipulating CIFTI Files Forum: open-discussion

RE: Extract Adjacency Matrix from Human Connectom Project MSMAll.dscalar.nii-file

Damon Pham — Thu, 27 Jul 2023 18:36:55 GMT

Hi Bas,
Thanks and sorry for the terribly delayed reply; I didn't know we had a Forums here!
With CIFTI data, spatial information is contained in a GIFTI file (*.surf.gii) which is separate from the CIFTI file having the measurements (*.dtseries.nii, *.dscalar.nii, *.dlabel.nii).
For HCP surface data at 32k, if you just want the vertex adjacency matrix, since all subjects are registered to a mesh with the same topology, you just need one file--and we've included it in ciftiTools: see `load_surf`. It will give a surface with the same topology as the ones used with the HCP. The `faces` component of the surface object returned by `load_surf` will give the three vertices in each face. To make an adjacency matrix: if a vertex shares a face with another vertex, it's adjacent, so collect for each vertex set adjacency to 1 for all other vertices it shares faces with, 0 otherwise. I might look into adding a function for this in our package.

RE: Error in header_cifti(cifti_fname) : Workbench command

Damon Pham — Thu, 27 Jul 2023 18:27:50 GMT

Hi elena,
Sorry for the terribly delayed reply; I didn't realize we had a Forums!
There's issues with reading CIFTI files stored on the cloud, sometimes. So if the package has been downloaded onto the cloud, reading files included in the package may fail. 
We're looking into a workaround that involves saving a copy of the desired to the disk as a temporary file, reading that in, then deleting the temporary file. Meanwhile, you may have to download the package to the disk, or implement this workaround yourself as necessary.

Extract Adjacency Matrix from Human Connectom Project MSMAll.dscalar.nii-file

basmats — Tue, 17 Jan 2023 15:37:59 GMT

Dear All,

For my master's thesis I am using R to fit a model to the working memory task fMRI dataset of the Human Connectome Project. To do so, I will need an adjacency matrix that marks the neighbors of each voxel. My supervisors and I have chosen to use the MSMAll.dscalar.nii files from the dataset. How can I extract this adjacency matrix from the file using ciftiTools? Or perhaps another package?

Best,

Bas

Error in header_cifti(cifti_fname) : Workbench command

Elena Aggius Vella — Fri, 05 Nov 2021 17:17:02 GMT

Hello
i m new with ciftiTool, i will really appreciate any help

i m trying to follow the tutorial but when i run the following line

xii <- read_cifti(
cifti_fname, brainstructures="all",
surfL_fname=surfL_fname, surfR_fname=surfR_fname,
resamp_res=4000
)

i get this error

Error in header_cifti(cifti_fname) :
Workbench command 'C:/PROGRA~1/workbench-windows64-v1.5.0/workbench/bin_windows64/wb_command.exe -nifti-information C:\Users\User\Dropbox\My\ PC\ \(Elena-DELL\)\Documents\R\win-library\4.0\ciftiTools\extdata/Conte69.MyelinAndCorrThickness.32k_fs_LR.dtseries.nii -print-header' failed.
Inoltre: Warning message:
In system(cmd, intern = intern, ignore.stdout = ignore.stdout, ignore.stderr = ignore.stderr) :
running command 'C:/PROGRA~1/workbench-windows64-v1.5.0/workbench/bin_windows64/wb_command.exe -nifti-information C:\Users\User\Dropbox\My\ PC\ \(Elena-DELL\)\Documents\R\win-library\4.0\ciftiTools\extdata/Conte69.MyelinAndCorrThickness.32k_fs_LR.dtseries.nii -print-header' had status 65535

thank you for every help
elena

Welcome to Open-Discussion

Damon Pham — Wed, 23 Jun 2021 20:40:20 GMT

Welcome to Open-Discussion