Yes, even if you did that and got it into the 2mm space correctly in FSL conventions (this is not easy), the absolute warp file will have near-zero values in one of the corners, even though the voxel that should have values close to 0 should generally be towards the center of the volume.
Tim On Thu, Jan 3, 2019 at 6:32 PM Glasser, Matthew <glass...@wustl.edu> wrote: > 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> > Date: Thursday, January 3, 2019 at 2:30 PM > To: Matt Glasser <glass...@wustl.edu> > Cc: Georgios Michalareas <g...@ae.mpg.de>, "hcp-users@humanconnectome.org" > <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> > 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 on behalf of >> Georgios Michalareas" <hcp-users-boun...@humanconnectome.org on behalf of >> 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 >> >phone: +49 69 8300479-325 >> >------------------------------------------------ >> > >> >_______________________________________________ >> >HCP-Users mailing list >> >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. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying or the taking of any action in reliance on the contents >> of this information is strictly prohibited. If you have received this email >> in error, please immediately notify the sender via telephone or return mail. >> >> _______________________________________________ >> HCP-Users mailing list >> 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. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
