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If you are using high resolution T1w and T2w images with FreeSurfer, you might just run the HCP Pipelines that depend upon such data and take care of all of this. Alternatively, you can see how FreeSurfer is called by the HCP Pipelines:

https://secure-web.cisco.com/1FyxUyuquU_ZJL3F2C8HzsVJtR4TjyEcfI1ujxzxMdtGJ9_... Lines 680 to 724

Matt.

On 2/25/22, 11:23 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tisdall, Dylan" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of mtisdall@pennmedicine.upenn.edu> wrote:

External Email - Use Caution

Hi all,

Thanks again for all the help so far with getting my data registered and surfaces extracted. I have one further issue that I'm hoping to get help with.

I've used bbregister to align my T2 scan with the surfaces from my T1 scan. However, the output is resampled down to 1mm iso and a 256^3 volume; I'd like to keep the native 0.8 mm resolution and FOV if possible (acknowledging, of course, there's actually some blurring in the interpolation, but just for the sake of nominal consistency).

I tried to work around this by applying the .lta output by bbregister to my T2 scan (with the goal of eventually using the --out-like flag to specify the sampling resolution, but not doing that yet):

mri_transform T2_SPACE.nii.gz T2_SPACE_transform.lta T2_SPACE_warped.nii.gz

However, when I load the resulting output volume (T2_SPACE_warped.nii.gz) in freeview, it has swapped axes. Strangely, this isn't the case with the output volume generated by bbregister... it's well-aligned with the surfaces. Similarly, if I load the T2_SPACE.nii.gz into freeview, and apply T2_SPACE_transform.lta as part of the load command, the volume is well-aligned.

So what's different about how mri_transform applies that .lta file, compared to bbregister and freeview?

Is there a way to just get bbregister to resample my T2 scan with the original resolution and FOV, so I can avoid applying mri_transform altogether? I don't see an --out-like option for bbregister, but is there a different flag?

Thanks again, Dylan

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