Hi,
Scripts do require some modification to work with the new FSL due to the
extra file format support. However, we have written several little helper
scripts to make life fairly easy. I've added a page to the FAQ that
describes
this. It is at:
https://www.fmrib.ox.ac.uk/fslfaq/scripting.html
Note that there are a couple of important things wrt your script.
First, you should get rid of all .hdr and .img extensions from the script.
Secondly, is that when you do the for loop over images and the subsequent
avwmerge, you will need to use "imglob -oneperimage" as described in
examples 3 and 5 on the page referenced above.
Thirdly, avwcreatehd has changed so that it always creates a zero filled
image now - which means that it will *OVERWRITE* your existing .img
files. Therefore, I would recommend using avwcreatehd to make a dummy
image (a different filename from everything else) then use avwcpgeom to
get the same image dimensions (if that is what this bit of the script is
meant
to do).
Hope this is clear enough.
Let me know if you have any more trouble.
All the best,
Mark
Jason Steffener wrote:
>Hello,
> I have been spatially normalizing and resampling images with FSL
>3.1 ANALYZE images and now I dont know what to do with the new image
>format. What I do is below, how do I now deal with the new image format?
>
>I tried just getting rid of the .img extensions in what I have below but
>it just resliced the images with the same resolution as the original.
>
> thank you,
> Jason.
>
>flirt -ref /usr/local/fsl/etc/standard/avg152T1_brain -in
>filtered_func_data -applyxfm -init example_func2standard.mat -out
>n_filtered_func
>
>avwcreatehd 45 54 45 1 4 4 4 3 22 32 18 2 temp
>
>cp n_filtered_func.img temp.img
>
>avwsplit n_filtered_func
>
>for fn in vol*.hdr;
>do flirt -ref temp -in $fn -out r$fn -applyxfm -init
>../../../fsl_html/id.mat;
>done
>avwmerge -t resample_n_run1 rvol*.hdr
>
>rm vol*.{img,hdr} rvol*.{img,hdr}
>rm temp.*
>
>
>
>
>Jason Steffener
>Department of Radiology
>New Jersey Medical School
>Biomedical Engineering Department
>New Jersey Institute of Technology
>Newark, NJ USA
>(973) 676-1000 x1545
>http://web.njit.edu/~jrs3
>
>
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