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Hello Mallory,
      It’s only step 2 that determines the registration target ( step 3 does carry out registration, but with the output of step 2. the -S/-T flags in step 3 only control how the skeleton is calculated ). However from your details below, something may have gone awry in step 2.

If you ran tbss_2_reg with the -T option, then target.nii.gz should be the FMRIB58 image ( 182x218x182 isotropic ). The file target_to_MNI152.nii.gz should not be created in this case, as the target is already in MNI152 space, and running an additional registration could cause some misalignment.

Can you confirm that target.nii.gz is identical to $FSLDIR/data/standard/FMRIB58_FA_1mm.nii.gz ? If it isn’t then I would recommend deleting your current outputs, and re-running toss_2_reg from the start.

Hope this helps,
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre 
John Radcliffe Hospital
University of Oxford

On 31 Mar 2020, at 20:20, Mallory Kisner <[log in to unmask]> wrote:

Hello,

I ran TBSS on 198 DTI images, then ran a 2-way between subjects ANOVA using randomise. I had intended to use the recommended -T tag to align to the FMRIB58 standard image in step 2, and the -S tag to align to the MNI152 image in step 3.

When looking at the results from my ANOVA mapped onto the MNI152 image, the alignment seems to be off. All of my data aligns well together and nothing appeared to be misaligned up to this point when checking after each step. But it is not mapping well onto MNI152 at the end. I am wondering if my data is usable as it aligns well within the dataset, and where something could have gone wrong?

Additionally, when looking at the dimensions of the target.nii.gz image, it seems that the dimensions do not match the MNI152 image. I do have a target_to_MNI152.nii.gz image in which the dimensions match, and each subject’s FA_to_target.nii.gz image matches the dimensions from MNI152 as well. Is it possible that the target.nii.gz image would change during one of these steps?

Any advice on whether this is still acceptable to use or where things may have gone wrong is greatly appreciated!

Thank you,
Mallory

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