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Hi, fslcc has a '-t' option, whose default value is 0.1, which probably means that any correlation values lower than 0.1 would not be displayed. If you want to display all correlation values, set the threshold to a very small value (for instance, 0.001). Best, Yang Hu At 2018-11-10 08:21:09, "Dawn Jensen" <[log in to unmask]> wrote: >Hi FSL gurus, > >I'm trying to see the correlations between different images and used fslcc, which mostly works, but seems to skip certain correlations for no particular reasons (visual inspection shows there is indeed overlap between the images, but it's not giving back a correlation value). I know this was originally intended to check correlations for MELODIC ICA and I am using it to check correlations between parallel ICA (GIFT, FIT). I'll list my full steps below: > >use fslchfiletype to convert the .hdr and .img files to .nii.gz >use fslmerge to create a 4D file, generally with three or four component images. (e.g. A.nii.gz, B.nii.gz, C.nii.gz) >use fslcc on two 4D files (e.g. fslcc A_C.nii.gz D_F.nii.gz) > >The output often will be: >1 1 .67 >1 3 .45 >3 2 .12 > >and there will be no information on the correlation with the 2nd element (or 3rd, seems random what gets left out). > >Weirdly enough, I can run "fslcc A_C.nii.gz H_K.nii.gz" and it will give correlation values for the image it had skipped previously, but skip others. Occasionally, it will give back correlations on all of the input. > >Any thoughts on what might be going on? Do I need to package the files differently? Is there a better way to do the comparison between images? >We are fine-tuning a pICA between grey and white matter changes in schizophrenia and would like to know how correlated components found in different iterations are with each other. > >Thanks in advance, > >Dawn Jensen >Neuroscience Dual Degree Program >Georgia State University >Research Assistant > >######################################################################## > >To unsubscribe from the FSL list, click the following link: >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1