I believe that FSL convertwarp converts between relative and absolute conventions, though the FSL coordinates issue might prevent that from being helpful.
Matt. From: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Date: Thursday, January 3, 2019 at 2:30 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: Georgios Michalareas <g...@ae.mpg.de<mailto:g...@ae.mpg.de>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Warping volume atlas and X, Y, Z of single point with standard2acpc_dc.nii.gz On Thu, Jan 3, 2019 at 10:47 AM Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: 1) FSL does not respect Workbench’s header info, so the labels get removed. You might need to use wb_command -volume-resample or copy over the header info. Yes, use wb_command -volume-warpfield-resample and the enclosing voxel method. 2) FSL has a utility to do this I believe (std2imgcoord), but it will be slow (we used to use this for warping surfaces before we had the wb_command. Not sure about the error message. The wb_command error message means what it says - the warpfield is a volume file, and any coordinates that are outside of its bounding box have a completely unknown warp, because there is no voxel in that location to tell it what the displacement vector is. There isn't a direct way to put a coordinate through a warpfield in workbench, but since you specifically want to transform a voxel grid through it, you can get there with a few tricks. First, convert the "native to standard" warpfield to "world" convention with wb_command -convert-warpfield - this convention gives at each voxel, the displacement that should be added to the coordinate (in proper nifti mm coordinates, rather than FSL's difficult conventions). You can then resample this to the 2mm space with wb_command -volume-affine-resample (use an identity affine, and probably trilinear resampling) to get the 2mm voxel grid you want. This is close, but the last step will need to be done manually, because the warpfield gives the relative displacement, but you want the absolute coordinate. So, in each voxel, you need to add the coordinates of the center of the voxel - there is no command to do this, so do it in matlab, or python, or... Matt. On 1/3/19, 10:31 AM, "hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> on behalf of Georgios Michalareas" <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> on behalf of g...@ae.mpg.de<mailto:g...@ae.mpg.de>> wrote: >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<mailto:g...@aesthetics.mpg.de> >phone: +49 69 8300479-325 >------------------------------------------------ > >_______________________________________________ >HCP-Users mailing list >HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> >http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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