I have a question regarding the usage of ciftify_statclust_report. I recently ran FSL’s MELODIC on my resting-state fMRI data to generate several independent components, and now I would like to identify the “peak vertex” for each cluster within each component, from which I will generate a set of ROIs. It is my understanding that ciftify_statclust_report with the –output-peaks flag would allow me to export a csv file with the cluster ID, location of the peak vertex, surface area of the cluster, mean intensity value, and atlas overlap, which would be ideal for my project! Unfortunately, I continue to receive several errors, and can’t seem to figure out what’s going wrong.
When I use the midthickness files generate from my data, along with the corresponding vertex-wise surface information like this:
I get a test_clust.dlabel.nii as output, which contains the thresholded clusters for each component, but there is no csv file. I also receive several errors:
Traceback (most recent call last):
File "/anaconda3/bin/ciftify_statclust_report", line 10, in
sys.exit(main())
File "/anaconda3/lib/python3.7/site-packages/ciftify/bin/ciftify_statclust_report.py", line 426, in main
ret = run_ciftify_dlabel_report(arguments, tmpdir)
File "/anaconda3/lib/python3.7/site-packages/ciftify/bin/ciftify_statclust_report.py", line 184, in run_ciftify_dlabel_report
label_data, surf_va_LR)
File "/anaconda3/lib/python3.7/site->packages/pandas/core/indexing.py", line 190, in setitem
self._setitem_with_indexer(indexer, value)
File "/anaconda3/lib/python3.7/site-packages/pandas/core/indexing.py", line 611, in _setitem_with_indexer
raise ValueError('Must have equal len keys and value '
ValueError: Must have equal len keys and value when setting with an iterable
When I run the same command, only with the default surface files (not specifying my own), I receive a different set of errors. However, I do get a test_clust.dlabel.nii file, a test_statclust_report.csv file, and a test_subcortical_peaks.csv file. Unfortunately, though, I can't seem to get the peak vertex location for the clusters on the surface (the subcortical file only has the subcortical clusters, and the report file doesn't have vertex location info).
Any thoughts/advice on how to troubleshoot this? I'm happy to send additional details regarding inputs, outputs, and error messages if need be. I'd also like to ask if I need to be running ciftify_statclust_report on each component of my ICA separately?
Hello,
I have a question regarding the usage of ciftify_statclust_report. I recently ran FSL’s MELODIC on my resting-state fMRI data to generate several independent components, and now I would like to identify the “peak vertex” for each cluster within each component, from which I will generate a set of ROIs. It is my understanding that ciftify_statclust_report with the –output-peaks flag would allow me to export a csv file with the cluster ID, location of the peak vertex, surface area of the cluster, mean intensity value, and atlas overlap, which would be ideal for my project! Unfortunately, I continue to receive several errors, and can’t seem to figure out what’s going wrong.
When I use the midthickness files generate from my data, along with the corresponding vertex-wise surface information like this:
I get a test_clust.dlabel.nii as output, which contains the thresholded clusters for each component, but there is no csv file. I also receive several errors:
When I run the same command, only with the default surface files (not specifying my own), I receive a different set of errors. However, I do get a test_clust.dlabel.nii file, a test_statclust_report.csv file, and a test_subcortical_peaks.csv file. Unfortunately, though, I can't seem to get the peak vertex location for the clusters on the surface (the subcortical file only has the subcortical clusters, and the report file doesn't have vertex location info).
Any thoughts/advice on how to troubleshoot this? I'm happy to send additional details regarding inputs, outputs, and error messages if need be. I'd also like to ask if I need to be running ciftify_statclust_report on each component of my ICA separately?
Thanks in advance!