Hi and Happy Hew Year,
I have 2 questions regarding warping a volume atlas and X,Y,Z coordinates of single points with the standard2acpc_dc.nii.gz warp. Excuse me If my questions are too naive. Here they are: Question 1: ====================================================================== I would like to transform the volume atlas file MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz from standard space to native space using the warp MNINonLinear/xfms/standard2acpc_dc.nii.gz I tried using "applywarp" 'applywarp --in=Atlas_ROIs.2.nii.gz --ref=T1_native.nii.gz --out=WARPED_Atlas_Native.nii.gz --warp=/mnt/beegfs/home/georgios.michalareas/workspace/projects/matthprob_MEG/data/smri/raw_nifti/BRS27/MNINonLinear/xfms/standard2acpc_dc.nii.gz --interp=spline' but in the resulting nifti there is no atlas label information . Question 2: ====================================================================== I would like to take the X,Y,Z coordinates of any voxel J in the 2mm template volume HCPpipelines-3.27.0/global/templates/MNI152_T1_2mm.nii.gz apply the standard2acpc_dc.nii.gz warping to them and get the new X,Y,Z coordinates of J in the native space. The reason I want to do this is to make a regular reference 2 mm grid from the corrdinates of the voxels of the 2mm template volume and warp each of the grid vertices to native space. I made a surf.gii file containing a pseudo-surface which had as vertices the coordinates of all voxels of the 2mm template MNI152_T1_2mm.nii.gz , and a dummy single face: g= faces: [1 2 3] mat: [4×4 double] vertices: [902629×3 single] I then applied wb_command -surface-apply-warpfield mrigrid.surf.gii Tfm_native2standard.nii.gz WARPED2NATIVE_mrigrid.surf.gii -fnirt Tfm_standard2native.nii.gz but I got the following error While running: /mnt/beegfs/home/georgios.michalareas/workspace/toolboxes/other/workbench-v1.3.2/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command -surface-apply-warpfield mrigrid.surf.gii Tfm_native2standard.nii.gz WARPED2NATIVE_mrigrid.surf.gii -fnirt Tfm_standard2native.nii.gz ERROR: surface exceeds the bounding box of the warpfield Is there a way to just transform any X,Y,Z of standard space to the corresponding X,Y,Z of Native Space. Thank you very much for your help Best Giorgos -- ------------------------------------------------ Dr. Georgios Michalareas Neuroscience Department Max Planck Institute for Empirical Aesthetics email: g...@aesthetics.mpg.de phone: +49 69 8300479-325 ------------------------------------------------ _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
