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Hi Mark, thanks for the reply. The problem is this (hopefully it will clarify), if I use flirt to create a linear registration of the mean of the functional data to the structural I get a matrix that cannot be applied by applywarp or applyxfm to the full functional data but I can do this with flirt. I couldn't work out why feat would do the registration but I couldn't do it by the command line so I ended up going through all the steps and seeing where it fails and it was at the first linear transform. I don't use fieldmaps either, we don't have them for this data :(. The problem seems to be that feat uses flirt to apply the concatenation of linear transforms whereas I was using applywarp and then after that did not work I tried applyxfm4d (I didn't know flirt could do this until I dug through the logs in feat). Could I clarify, for future reference, if I use field maps with epi_reg do I get a .mat file that is a warp or a .nii.gz file as normal? My files aren't that big, I got confused by the log in feat as it says it's using hi-res images but it just means T1's so that's where the hi-res bit came from. I am using ~600mb or less files at 64x64x64 as you say. I also use 2mm space. I don't think that should be a problem? Maybe you could try the matrix above. I don't know why it would be doing this. The matrix doesn't look that contorted and I don't really have problems with any other files. Thanks, Tom On Fri, May 2, 2014 at 9:14 AM, Mark Jenkinson <[log in to unmask] > wrote: > Hi, > > When you use bbr with fieldmaps then the transformation is non-linear > rather than linear. I cannot tell from your email if you are using > fieldmaps or not, but I will assume you are. In that case then only flirt > and applywarp are capable of applying the correct transformation. The > epi_reg script should write out an appropriate warp for applywarp. So I'm > not sure what you mean by applywarp does not work but flirt alone does. > Applyxfm4D is not intended for non-linear transformations and this should > not be used if you have fieldmaps. > > The reason it is using all of your memory might be due to the size of > your timeseries. The epi_reg script tries to apply the warp to the whole > 4D dataset, and this may be large, depending on your images, as going to > MNI space (especially the 1mm or 0.5mm versions) will *really* increase the > size of the images. For instance, if your functional images were > 64x64x64x300 then the file size would be about 600MB (as each value is > typically stored with 8 bytes). However, if you resampled to the 1mm MNI > space, which is 182x218x182, then the file size would become 16GB! And > given that most programs require two copies of something in memory at some > point during their execution, this means that it will probably slow down or > crash on a machine with less than 30GB of memory. > > The second paragraph above would also apply to the non-fieldmap case, > with just linear transformations, as you are still trying to create a very > large file. > > If you really need to create a high-resolution standard space version of > your image then you probably need to use a machine with a lot of memory. > Alternatively, you might think about resampling to a lower-resolution > standard space, such as a 3mm or 4mm resolution, which is often what is > done for ICA analyses. > > I hope this helps. > All the best, > Mark > > > > On 1 May 2014, at 18:01, Thomas Nickson <[log in to unmask]> wrote: > > I've noticed that this can be applied with flirt and flirt alone, > applywarp and applyxfm4d does not work. Seems to be a bug. > > > > On Thu, May 1, 2014 at 4:46 PM, Thomas Nickson <[log in to unmask]>wrote: > >> Hi All, >> >> I have been trying to register some functional images to mni space. I >> have used a number of methods but I have found that if I use standard >> functional and structural images and put them in epi_reg then at the stage >> of applying the linear transformation from the non-bbr flirt it eats all of >> the machines ram and is then killed. It's only this one file but I don't >> understand why it happens. >> >> If I run it using applyxfm4d instead it doesn't use all of the ram >> instantly but it's been running for over an hour and is increasingly using >> all the ram. I suspect it is just a slower version of the same problem. >> >> The mat file doesn't look too strange but maybe someone else has had this >> problem or knows what I am doing wrong. I have tried feat which seems to >> use the same method, just running epi_reg but with the added step of >> generating hi-res structural images, and this seems to work but running >> epi_reg alone does not. It crashes. >> >> 0.9999879953 -0.004211583523 0.002482311973 1.383813017 >> 0.004258561284 0.99980606 -0.01923345401 -6.171911295 >> -0.00240082707 0.01924379718 0.9998119479 62.65789894 >> 0 0 0 1 >> >> Any help appreciated, >> > > >