Something that just bit me: you should probably specify "--rel" on convertwarp and applywarp, because wb_command doesn't currently understand the absolute warpfield convention that seems to be the default.
Tim On Fri, Feb 2, 2018 at 10:07 PM, Timothy Coalson <tsc...@mst.edu> wrote: > I have this working using c3d (I didn't use its fsl conversion, but it > would probably work and save two steps, as the inversion wouldn't be > needed). The important bits follow. > > Tim > > c3d_affine_tool -itk ants_warpAffine.txt -o ants_affine_world.txt > > #the affine it outputs is reverse (atlas coords to individual coords) > #wb_command world convention is a forward warp, so the output of the > wb_command conversion is the inverse of what fsl needs > wb_command -convert-affine \ > -from-world ants_affine_world.txt \ > -to-flirt "$subjdir"/ants_affine_flirt.txt \ > "$templatedir"/MNI152_T1_0.7mm.nii.gz \ > "$insubjdir"/T1w/T1w_acpc_dc_restore.nii.gz > convert_xfm \ > -inverse "$subjdir"/ants_affine_flirt.txt \ > -omat "$subjdir"/ants_affine_inv_flirt.txt > > #apply X and Y flips to warpfields > #first negate all of them, then take the frames I need > wb_command -volume-math '-x' \ > ants_warponly_negative.nii.gz \ > -var x ants_warpWarp.nii.gz > > wb_command -volume-merge \ > ants_warponly_world.nii.gz \ > -volume ants_warponly_negative.nii.gz \ > -subvolume 1 -up-to 2 \ > -volume ants_warpWarp.nii.gz \ > -subvolume 3 > > #affine already takes it into MNI space, so use MNI as ref for both sides > of warp > wb_command -convert-warpfield \ > -from-world ants_warponly_world.nii.gz \ > -to-fnirt "$subjdir"/ants_warponly_fnirt.nii.gz \ > "$templatedir"/MNI152_T1_0.7mm.nii.gz > > #compose > convertwarp \ > --ref="$templatedir"/MNI152_T1_0.7mm.nii.gz \ > --premat="$subjdir"/ants_affine_inv_flirt.txt \ > --warp1="$subjdir"/ants_warponly_fnirt.nii.gz \ > --out="$subjdir"/ants_fullreg_fnirt.nii.gz > > #resample to sanity check > applywarp \ > --ref="$templatedir"/MNI152_T1_0.7mm.nii.gz \ > --in="$insubjdir"/T1w/T1w_acpc_dc_restore.nii.gz \ > --warp="$subjdir"/ants_fullreg_fnirt.nii.gz \ > --out="$subjdir"/ants_reg_fnirt_resamp.nii.gz > > > On Fri, Feb 2, 2018 at 5:41 PM, Moises Hernandez Fernandez < > mois...@fmrib.ox.ac.uk> wrote: > >> I had the same problem in the past... try: >> *c3d_affine_tool -itk ANTSmat.txt -ref myref -src mysrc -ras2fsl -o >> FSLmat.txt * >> >> However, as Tim said, this tool only converts the affine, not the warp. >> >> Moises. >> >> >> >> On 2 February 2018 at 18:33, Timothy Coalson <tsc...@mst.edu> wrote: >> >>> I haven't finished figuring this out, but it appears that the affine >>> file's "Parameters" array contains the 12 affine components you'd find in a >>> normal affine file. The warpfield does not seem to include the affine, so >>> you need to convert and use both of them, which may be why what you did >>> looked wrong. >>> >>> Tim >>> >>> >>> On Fri, Feb 2, 2018 at 4:54 PM, Glasser, Matthew <glass...@wustl.edu> >>> wrote: >>> >>>> I think Tim Coalson might be playing with this right now. Perhaps he >>>> can respond if there is a solution he figures out. >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Anjani >>>> Bhargavi <anjaniragotha...@gmail.com> >>>> Date: Friday, February 2, 2018 at 4:36 PM >>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>>> Subject: [HCP-Users] Software to convert ANTs warps to FSL format >>>> >>>> Hi, >>>> >>>> Have any of you tried converting ANTs warps to FSL format? I tried >>>> doing it with c3d_affine_tool -ras2fsl option, but I wasn't not successful >>>> with it. I ended up with an error: >>>> >>>> terminate called after throwing an instance of 'char const*' >>>> >>>> Aborted (core dumped) >>>> >>>> >>>> I actually would like to convert the nonlinear warps. If there's a tool >>>> that any of you have used to do that, please let me know. I tried using the >>>> workbench command, convert-warpfield, to convert from world to fnirt >>>> format. The command worked, but when I used the warp to do the >>>> registration, the output didn't look like it actually worked. Any help is >>>> appreciated. >>>> >>>> -- >>>> Thanks and Regards, >>>> Anjani Bhargavi.R >>>> If you have the willpower to do things nothing will be against you! >>>> >>>> _______________________________________________ >>>> HCP-Users mailing list >>>> HCP-Users@humanconnectome.org >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> >>>> _______________________________________________ >>>> HCP-Users mailing list >>>> HCP-Users@humanconnectome.org >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> HCP-Users@humanconnectome.org >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >> >> > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
