I used afni_proc.py to process my data, followed by registration to a template using ANTS. Data looked normal up until this point. I then ran functional connectivity analysis on the data, including 3dfim+. the images output by this command look like this with some voxels with an Olay value of 0, which doesn’t seem right. Does anyone know why that would happen or how to fix it? Thank you.
What commands did you use for the functional connectivity?
Can you post your code?
#L nACC # extract timecourse of L nACC 3dmaskave -quiet -mask ../../Zach_ROIs_onepointfive.nii -mrange 43 44 $1.Entropy.Mood_MOTIONpreprocessed/ANTified_errts_onepointfive.nii.gz > bilat_nACC_timecourse15.txt #Enforce a TR structure on the data (IMPORTANT!!! Otherwise 3dfim+ in the next step will barf) 3drefit -TR 2.0 $1.Entropy.Mood_MOTIONpreprocessed/ANTified_errts_onepointfive.nii.gz #Create functional connectivity map 3dfim+ -input $1.Entropy.Mood_MOTIONpreprocessed/ANTified_errts_onepointfive.nii.gz -polort 0 -ideal_file bilat_nACC_timecourse15.txt -out Correlation -bucket bilat_nACC_Corr15 # convert to z scores 3dcalc -a bilat_nACC_Corr15+orig. -expr 'log((1+a)/(1-a))/2' -prefix $1.Entropy.Mood_MOTIONpreprocessed/bilat_nACC_Corr15map_z
Without the data, it is difficult to say for sure. Guesses:
[li] 3dfim+ is very very old – I don’t know if it is still “good”. Try 3dTcorr1D instead.
[/li][li] Is it possible ANTS left a “hole” in the data when transforming it (that is, created a voxel with all zero entries)? It would be necessary to look at the transformed time series dataset (input to 3dfim+) at a location where the correlation was 0 to investigate the answer to this question.
Without more information, I don’t know what else to say.
using 3dTcorr1D seems to have solved the problem. thank you!
Sorry to take so long to check back…
Another option (that I use) is 3dNetCorr.
with the -ts_wb_Z option
I find it a little faster if you have many ROIs.