Dear Sara,

I suspect this might be caused by a bug in the 6.0.1 release. In the past flirt would only read the first volume of the -ref image, and then resample the -in image to that. In 6.0.1 it reads all volumes in the -ref image (35 volumes) and resamples all the -in volumes (35) to each of the 35 -ref volumes, resulting in 35x35=1225 volumes.

If you do

fslroi DTI.nii.gz tmpvol 0 1
flirt -in tmpvol -ref reference_DTI.nii.gz -o DTI_resampled.nii.gz -applyxfm

it should work the way you expect it to.

Jesper



On 19 Jun 2019, at 20:45, [log in to unmask] <[log in to unmask]> wrote:

Hi FSL team,

I am using eddy_cuda to preprocess my DTI image (32 directions and 3 b0 volumes). Since my computer has limited memory, I cannot preprocess images with a high dimension of 256*256*74*35. I tried to downsample them using a reference image using this command:

flirt -in DTI.nii.gz -ref reference_DTI.nii.gz -o DTI_resampled.nii.gz -applyxfm


Now that I use fslinfo to look at the DTI_resampled.nii.gz, the dimensions are 100*100*74*1225.


How can I ensure that I have 35 volumes rather than 1225.


Thanks,

Sara



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