rcruces
commented
1 year ago Hello, this is the expected behavior of the current version of the pipeline. We are storing the connectomes as GIFTI files because they use less storage and contain metadata about the creation. You can load the gifti files using different software like R, python of matlab. Below is an example with python:
import nibabel as nb
def load_sc(File):
"""Loads and process a structura connectome
File is the path to the gifti file
"""
# load the matrix
mtx_sc = nb.load(File).darrays[0].data
# Mirror the matrix
mtx_sc = np.log(np.triu(mtx_sc,1)+mtx_sc.T)
mtx_sc[np.isneginf(mtx_sc)] = 0
# replace 0 values with almost 0
SC[SC==0] = np.finfo(float).eps
return SC
araikes
What is the current behavior?
I ran, in sequence,
-proc_structural,-proc_surf,-post_structural,-proc_dwi, and then-SC. The connectomes folder is populated only with the.giifiles and no text files. The log file does not indicate any errors or failures.What is the expected behavior?
I anticipated seeing text files with the edge length connectomes.
Please tell us about your computing environment: Singularity, micapipe v0.2.0.
singularity run --cleanenv -B /xdisk/adamraikes/cornell/nifti:/nifti:ro -B $PWD/derivatives:$PWD/derivatives -B /tmp:/tmp -B /groups/adamraikes/license.txt:/license.txt /groups/adamraikes/singularity_images/micapipe_v0.2.0.sif -bids /nifti -out $PWD/derivatives/micapipe -sub 087 -tmpDir /tmp -SC -tracts 20M -fs_licence /license.txtLog file attached: log.txt DWI connectome folder: