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Hi, I tried your method and compared with results from other software packages (AFNI and ANTs). FSL: flirt -in $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz -ref $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz -applyisoxfm 3 -noresampblur -out FSL_MNI152_T1_3mm_brain.nii.gz AFNI: 3dresample -dxyz 3.0 3.0 3.0 -prefix AFNI_MNI152_T1_3mm_brain.nii.gz -inset $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz ANTs: ResampleImage 3 $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz ANTs_MNI152_T1_3mm_brain.nii.gz 3x3x3 0 0 I found that three softwares give different results. The final image size is 60*72*60 in FSL, while that is 61*73*61 in AFNI and ANTs. There are other differences among these resampled images. Is there a standard to determine which one is correct? I think this might be an important issue, because we normally report results in MNI152 standard space and there couldn't be different standard spaces？ Best, Yang Hu At 2018-05-09 22:47:55, "Matthew Webster" <[log in to unmask]> wrote: >Hello, > If you just want an isotropic resample then the input image can also be the reference, e.g.: > >flirt -in $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz -ref $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz -applyisoxfm 4 -out foo > >Kind Regards >Matthew >-------------------------------- >Dr Matthew Webster >FMRIB Centre >John Radcliffe Hospital >University of Oxford > >> On 9 May 2018, at 08:57, huyang <[log in to unmask]> wrote: >> >> Hi, >> >> Thank you! I find that the solutions listed in the post could not solve my problem, if I don't miss something. The post lists two methods: flirt and ApplyXFM, and ApplyXFM would invoke flirt internally. The key is a reference image which is exactly placed in the space I want. However, I just don't have this kind of reference image and it seems a chicken-and-egg problem. I could manually create a reference image, but it would be error-prone. >> >> Best, >> Yang Hu >> >> At 2018-05-09 14:59:53, "Ort, E." <[log in to unmask]> wrote: >> Hi, >> >> this post should help you: >> >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1302&L=fsl&D=0&P=499466 >> >> Just pick a reference an image that is in the same space as you want your image to be. >> >> Good luck, >> >> Eduard >> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of huyang [[log in to unmask]] >> Sent: 09 May 2018 05:43 >> To: [log in to unmask] >> Subject: [FSL] change voxel size of MNI T1 template >> >> Dear experts, >> >> I would like to resize the MNI152 T1 template to a lower resolution (for example, 3mm) and how can I do this using commands? I find the melodic GUI has a "resampling resolution" option, but I don't know how to do this with commands. I could use other software (for example, AFNI) to do this, but I am wondering if there is an FSL alternative. >> >> Best, >> Yang Hu >> >> >> >> >> >>