resampling of subcortical ROI

[Namrata Tamang]

Dear HCP team,

 I am working with subcortical ROIs  (CA1 and Subiculum-freesurfer seg) and would like to convert them into CIFTI space. I came across Tim’s note in a thread:

Following this, I attempted resampling using the command below:

wb_command -volume-resample   ca1_roi.nii   MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz ENCLOSING_VOXEL  ca1_roi_resampled.nii   \

 -warp T1w/BrainExtraction_FNIRTbased/str2standard.nii.gz   -fnirt T1w/T1w_acpc.nii.gz

Could you please confirm if this is the correct way to resample? I would like to confirm: whether the overall approach is correct and input files for <volume-space>, -warp, and -fnirt are appropriate. 

Thank you.

Best regards,

Namrata

[Tim Coalson]

I think our freesurfer space should be the same volume coordinates as our T1w rigid-aligned space (it is only their surface formats that have strange coordinates), which means the warp to get to MNINonLinear space is MNINonLinear/xfms/acpc_dc2standard.nii.gz .  That argument to -fnirt should be fine.  The 91k grayordinates use MNINonLinear space for the subcortical data.

You can use the ".nii.gz" extension for all your wb_command volume file outputs to save some disk space.

Tim

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[Namrata Tamang]

Dear Tim,

Thank you for you prompt reply!

Namrata