Thanks much Tim! I'll give it a try. On 2 February 2018 at 20:36, Timothy Coalson <tsc...@mst.edu> wrote:
> 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 >>>> >>> >>> >> > -- 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
