Hi,

We find that invwarp can take a very long time if either
there is a particularly large FOV in the t1_brain (is there
a lot of space around the brain in the image?) or if the
resolution is very high.  It always helps to crop the
original brain image down (just leave the brain but not
much surrounding space - like the MNI152 images).
However, if it is largely because of high resolution then
it may be quite slow.  We are working on some ways of
speeding this up, but at the moment the best options are
to do the cropping (and you'll need to run fnirt again)
and/or downsample the t1_brain image (e.g. with ApplyXFM)
to a lower resolution just for the invwarp step, and then use the
higher resolution one for the applywarp.

I'm not sure what is going wrong in the second case.
Can you please send us your command lines for
invwarp and applywarp?  It should be possible to
get the invwarp output to work fine with applywarp.

All the best,
	Mark





On 22 Jan 2009, at 17:50, Ryan Muetzel wrote:

> Hello,
>
> We are having a few problems with the FNIRT and invwarp tools.
>
>
> 1.) We are attempting to register our T1 image (1mm isotropic
> voxels) to the MNI152_2mm_brain using FNIRT, and then use invwarp to
> invert the warp field. The FNIRT step works fine, but when we use
> invwarp, it takes 20+hrs and usually crashes. Instead of using
> invwarp, we have tried running FNIRT to align the MNI152_2mm_brain
> to our T1, and that works fine. We are using CentOS5 on a dual core
> AMD opteron with 8gb of RAM. Here are the commands we are running:
>
> fnirtcfn=$FSLDIR/src/fnirt/fnirtcnf/T1_2_MNI152_2mm.cnf
> $FSLDIR/bin/fnirt --in=t1_brain --ref=$FSLDIR/data/standard/
> MNI152_T1_2mm_brain --aff=t1_to_MNI152_2mm_lin.mat --
> cout=t1_to_MNI152_2mm_warp_coeff --iout=t1_to_MNI152_2mm_nonlinear --
> fout=t1_to_MNI152_2mm_fout --logout=t1_to_MNI152_2mm_nonlinear.log --
> config=$fnirtcfn
>
> $FSLDIR/bin/invwarp -w t1_to_MNI152_2mm_warp_coeff -o
> MNI152_2mm_to_t1_coeff_warp -r t1_brain
>
>
> 2.) The second issue we are seeing is when we attempt to obtain the
> inverse of a DTI (2mm x2.5mm x 2.5mm voxels) -> FMRIB58_FA_1mm
> alignment. We are using the same hardware and commands as I
> mentioned above (except we are using the DTI FA map and the
> FMRIB58_FA_1mm as --in and --ref). As before, FNIRT works very well
> in both directions (FAmap ->FMRIB58 and FMRIB58 -> FAmap). In this
> case, the invwarp of FAmap->FMRIB58 only takes about 45min. However,
> the images resulting from applywarp are not correct, and I am unsure
> if it is a problem with applywarp or invwarp (see attached jpeg).
> Because I am not seeing this problem with 2mm isotropic DTI data, I
> tried resampling these data, but that didn't work either.
>
> Do you see any problems with the FNIRT and invwarp steps we are
> doing? Instead of using invwarp, would you suggest only using FNIRT
> for these alignments, to get around these issues (i.e., native data -
> > standard and standard -> native data)?
>
> Any suggestions would be greatly appreciated!
>
> -Ryan
>
> <bad_alignment.jpg>