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help > RE: CC200.1D from ABIDE I
Sep 16, 2024 04:09 PM | Tamsin Rogers
RE: CC200.1D from ABIDE I
Hi Cherry,
Based on the publication dates, it
looks like the ABIDE I preprocessed C-PAC pipeline was run with a
C-PAC version around 0.3.9.1. In that version of C-PAC, there are
two steps from the preprocessed functional image to the 1D ROI
timeseries output:
- resample
the preprocessed file into the space of the atlas (
flirt -in Caltech_0051458_func_preproc.nii.gz -ref cc200_roi_atlas.nii.gz -out Caltech_0051458_func_preproc_flirt.nii.gz -omat Caltech_0051458_func_preproc_flirt.mat -applyxfm -init ident.mat -interp trilinear) -
run this Python function to extract mean
of voxel across all timepoints for each node in the ROI mask. That
code is pretty old and in Python 2, but by bringing it up to Python
3 as shown in the attached file:
The 1D file generated from that function (with the output from
step 1 as data_file and cc200_roi_atlas.nii.gz from s3://fcp-indi/data/Projects/ABIDE/Resources/cc200_roi_atlas.nii.gz as
template) is identical to s3://fcp-indi/data/Projects/ABIDE/Outputs/cpac/filt_global/rois_cc200/Caltech_0051458_rois_cc200.1D
Our team can continue looking into other reasons why a current C-PAC image wouldn't generate the same 1D file - let me know if this helps in the meantime!
Threaded View
| Title | Author | Date |
|---|---|---|
| cherry ye | Aug 20, 2024 | |
| Tamsin Rogers | Sep 16, 2024 | |