Hi,
I've been trying to set up hcp_fix, but have not been getting the proper output. In running hcp_fix, I get the output volume file of ${run}_hp2000.nii.gz, and the ${run}_hp2000.ica directory is produced, but I am not getting the files ${run}_Atlas_hp2000_clean.dtseries.nii or ${run}_hp2000_clean.nii.gz to use in analysis. Everything seems to be running fine, and I cannot find where in hcp_fix of fix itself these files are produced, just where they are renamed and moved. May I ask if you have any suggestion of what may be going on here and how I can get the output I need? Would be very helpful.
For reference, this is the output printed to the terminal:
[mid2018@node142 Results]$ $FSL_FIXDIR/hcp_fix $run/${run}.nii.gz 2000
processing FMRI file TGNG3 with highpass 2000
running highpass
running MELODIC
running FIX
FIX Feature extraction for Melodic output directory: TGNG3_hp2000.ica
create edge masks
run FAST
registration of standard space masks
extract features
FIX Classifying components in Melodic directory: TGNG3_hp2000.ica using training file: /home/caseylab_curate/software/fix1.06/training_files/HCP_hp2000.RData and threshold 10
FIX Applying cleanup using cleanup file: TGNG3_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup set to 1
Thank you very much,
Michael
|