Dear Asa,
Rather than resampling to 2mm and then applying a linear transform, I would first transform and then resample.
Cheers,
Juan Eugenio Iglesias www.jeiglesias.comhttp://www.jeiglesias.com
On Aug 9, 2022, at 3:32 PM, Asa Borzabadi Farahani <asa.borzabadifarahani@mail.mcgill.camailto:asa.borzabadifarahani@mail.mcgill.ca> wrote:
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Hi,
I hope this email finds you all well.
I have a basic question about the right way of using ThalamicSegmentation method ( implemented by Iglesias et al. 2018). I plan to use this subject-specific atlas on the data processed via the HCP pipeline.
In this regard, after doing the PreFreeSurfer and Freesurfer bash files introduced by the HCP team, I use the subject-specific folder created by FreeSurfer and run the SegmentThalamicNuclei on the data of the subject.
The point is that, HCP pipeline ultimately converts all timeseries into CIFTI format ( subcortical areas in 2mm template), hence the mgz file created by the SegmentThalamicNuclei bash file, should be converted into the CIFTI to be useful when defining ROIs. So, I am using the following commands to get the subject-specific thalamic labels in the CIFTI space.
Could anyone having more experience confirm if it is a reasonable way or help if there exists a more accurate option?
Regards, Asa Farahani
mri_convert -rt nearest -rl /029/T1w/T1w_acpc_dc_restore.nii.gz /029/mri/ThalamicNuclei.v13.T1.mgz ThalamicNuclei029.v13.T1.nii.gz
applywarp --rel --interp=nn -i ThalamicNuclei029.v13.T1.nii.gz -r /029/MNINonLinear/T1w_restore.nii.gz -w /029/MNINonLinear/xfms/acpc_dc2standard -o ThalamicNuclei029.v13.T1.native.nii.gz
applywarp --interp=nn -i ThalamicNuclei029.v13.T1.native.nii.gz -r /029/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz -o ThalamicNuclei029.v13.T1.Atlas_2mm.nii.gz
wb_command -volume-label-import ThalamicNuclei029.v13.T1.Atlas_2mm.nii.gz FreeSurferColorLUT.txt ThalamicNuclei029.v13.T1.Atlas_2mm.nii -drop-unused-labels wb_command -cifti-create-dense-from-template template..dlable.nii T029.dlabel.nii -volume-all ThalamicNuclei029.v13.T1.Atlas_2mm.nii.gz
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