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April 13, 2021 06:12PM
I would like to use Freesurfer aseg atlas (aparc.a2009_aseg.nii) in the subject space. I think I'm so close and I found other posts related to this, but I can't still figure out how to get the atlas in the native space.

I ran @SUMA_Make_Spec_FS (command I ran: @SUMA_Make_Spec_Fs -NIFTI -sid sub-01), and it created the SUMA directory, which has subj_SurfVol.nii and aparc.a2009s+aseg.nii (all beautiful!).

I found that sub-01_SurfVol.nii has 256, 256, 256 voxels (x,y,z) but my subject's native T1 (say sub-01_T1w+orig) has 176, 256, 256 voxels, so I ran @SUMA_AligntoExperiment with sub-01_T1w+orig as exp_anat input. It created sub-01_SurfVol_Alnd_Exp+orig, but this one and aparc.a2009s+aseg.nii is still in 256/256/256 voxel space.

When I ran 3dresample to align aparc.a2009s+aseg.nii to align it to my native space, it didn't align well. I think I could try 3dallineate, but I feel like I might be just missing something or not doing the first step in a correct way because, in other posts, I saw comments saying that the output from @SUMA_Make_Spec_Fs should be in the exact native space.

Could you give me any advice on this? Also, I'm generally confused 1) whether sub-01_SurfVol+orig is supposed to be in the native (T1) space (rectangle-like space) or in a freesurfer-ish space (square-like space where all dimensions have the same number of voxels), and 2) whether the output of @SUMA_AlignToExperiment is supposed to be in, in the native space.

Thank you!!
Subject Author Posted

Freesurfer aseg from @SUMA_Make_Spec_FS in native space

irenej24 April 13, 2021 06:12PM

Re: Freesurfer aseg from @SUMA_Make_Spec_FS in native space

ptaylor April 14, 2021 09:31AM

Re: Freesurfer aseg from @SUMA_Make_Spec_FS in native space

irenej24 April 14, 2021 11:17AM

Re: Freesurfer aseg from @SUMA_Make_Spec_FS in native space Attachments

irenej24 April 14, 2021 11:28AM

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