 |
 |
Dear FSL experts, I have ran into a strange problem that I have been stuck at for sometime and would like some help:) I am running a single subject ICA as a QC for my denoising strategy. below is the command that I ran: melodic -i $inputfile -o $outputdir/$subject --nobet -a concat --report --Oall -m MNI152_T1_2mm_brain_mask.nii.gz. Since I switched on --Oall function, I have the stats folder with the thresholded zstats map for each component, which shows that my dataset has surviving significant clusters for the component after thresholding. However, in the report folder, the corresponding IC_thresh.png is blank . I have found this only happens when the $inputfile is smoothed, and does not happen when it's not smoothed. Below is the denoising strategy that I applied. 1) fsl_regfilt noise signal calculated by fmriprep (aroma estimated motion artifacts, signal from CSF and white matter, dvars, acomcor, frame displacement, linear detrend) 2) calculate temporal mean (fslmaths -Tmean) after regressing out the above noise. 3) 3dBandpass filtered signal to 0.01 0.08 4) added back temporal mean to bandpass signal 5) Smoothing (using Broccoli) with kernel of fwhm 6mm. Up to step 4) I am able to generate non-empty IC_thresh.png, however, after smoothing is applied, IC_thresh.png is empty even though zstats map is not. Does anybody know what went wrong? Also, as a side note, I have seen people adding temporal mean back to bandpass signal(step 4), but personally I am not certain about the rational behind this. Does anybody have any opinion on this? Thank you! Regards, Jiayi ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1