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

Reply via email to