Thanks!
Emily
----- Original Message -----
From: Andreas Bartsch <[log in to unmask]>
Date: Wednesday, February 20, 2008 3:49 pm
Subject: [FSL] AW: [FSL] McFLIRT basic use question
> 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
>
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