Hi, <br>I am trying to use fslmaths to filter my data before I plug it into a resting state analysis. However, once I obtain a pcc map, all correlation coefficients are &lt;0.1, even the autocorrelation with the seed voxel. <br>
The data look fine when I open them in Matlab using MRIread; the correlations between individual voxel time courses obtained in Matlab is about 0.6. <br><br>My analysis stream is as follows: <br>a) I filter the data using &quot;fslmaths input -bptf highpass lowpass output&quot;; from this I obtain a filtered nii.gz file<br>
b) I extract a seed timecourse from the filtered data in Matlab<br>c) I run mkanalysis-sess with -notask <br>d) I run selxavg3-sess<br>e) I overlay the pcc.nii <br><br>I have tried this with smoothed and unsmoothed data, with and without nuisance regressors, with different seeds, with mri_convert after step a. It is not a problem with the overlay since the max values in pcc are all &lt;0.1. <br>
I noticed that there are some differences in the nifti header (as read with MRIread) before and after filtering, but it seemed to me that they are gone after I used mri_convert. <br>I do find much higher correlations with unfiltered data. <br>
Any advice what could be going wrong here? I am using Freesurfer 5.1 and FSL 4.1.9 on Linux. <br>Thanks, Caspar<br><br>