 |
 |
Hi, >a) do we use the Motion Corrected images for our processing? you can but in my experience mcflirt is more robust. >b) do we then do McFLIRT on those images? No: if you use the Moco images from the scanner you should NOT run mcflirt on top (simply because it will degrade your images). Cheers- Andreas ________________________________ Von: FSL - FMRIB's Software Library im Auftrag von Emily Stoneham Gesendet: Mi 20.02.2008 18:40 An: [log in to unmask] Betreff: [FSL] McFLIRT basic use question Good Afternoon! This is a basic question regarding use of McFIRT. Our Scanner puts out both a file of the DICOM images per run (290 volumes, 30 slices per image) and a file that is motion corrected by the scanner (same image numbers as above). I then convert these to .nii using MRIConvert, and reorient the images using a script provided to me by Mark Jenkinson. I would like to know: a) do we use the Motion Corrected images for our processing? b) do we then do McFLIRT on those images? Assuming we do a McFLIRT prior to doing Slice Timing: c) I have been having a hard time figuring out how to batch those 290 images so that it does a McFLIRT on each one. I would like to stay within FSL to do this (I had been advised to do this in another program like AFNI), as it would greatly simplify things. I have a batch file for reorienting images (works amazingly well- thank you Mark!): for fn in *.nii ; do fslswapdim $fn -x y -z swapped_$fn ; done ... BUT I can't extrapolate how to do this kind of thing for McFLIRT - i.e., something that I can also apply to slice timing and 4D conversion (no, I don't know Unix other than basic commands). Can someone give me a hint as to the basics of batch filing (if that is what it is called) in FSL? Cheers! Emily