Oh wow. thank you very much. You just save me weeks worth of work. On Tue, Jan 16, 2018 at 2:31 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
> FYI > > ---------- Forwarded message ---------- > Date: Tue, 16 Jan 2018 19:59:38 +0000 > From: Mark Jenkinson <mark.jenkin...@ndcn.ox.ac.uk> > To: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Longitudinal Pipeline > > Hi Aaron and Hi Bruce! > There is code to convert ANTs format to FSL, so you can use that. > It is part of this tool: > https://sourceforge.net/p/c3d/git/ci/master/tree/doc/c3d.md > > I've included a code snippet below to show how we've used this. > Cheers, > MJ > > ${antsFolder}/antsRegistrationSyN.sh -d 3 -f ${ref} -f ${ref2} -m ${src} > -m ${src2} -o > ${workdir}/${outname}_ -t 'b' -j 1 > > ${c3dFolder}/c3d_affine_tool -ref ${ref} -src ${src} -itk > ${workdir}/${outname}_0GenericAffine.mat > -ras2fsl -o ${workdir}/${outname}_affine_fsl.mat > > ${c3dFolder}/c3d -mcs ${workdir}/${outname}_1Warp.nii.gz -oo > ${workdir}/wx.nii.gz > ${workdir}/wy.nii.gz ${workdir}/wz.nii.gz > ${FSLDIR}/bin/fslmaths ${workdir}/wy -mul -1 ${workdir}/i_wy > ${FSLDIR}/bin/fslmerge -t ${workdir}/${outname}_warp_fsl ${workdir}/wx > ${workdir}/i_wy ${workdir}/wz > > ${FSLDIR}/bin/convertwarp --ref=${ref} --premat=${workdir}/${outname} > _affine_fsl.mat > --warp1=${workdir}/${outname}_warp_fsl --out=${workdir}/${outname}_wa > rp_fsl > ${FSLDIR}/bin/invwarp -w ${workdir}/${outname}_warp_fsl -o > ${workdir}/${refBN}_to_${srcBN}_warp_fsl > -r ${src} > > > > On 15 Jan 2018, at 15:18, Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: > > Hi Aaron > > we compute the warp and save it in the mri/transforms/talairach.m3z, but > don't apply it (so > don't require an extra resampling). I know we have some tools around to > convert to ANTS > format, but I'm not sure about fnirt. I'll cc MJ who may know (hi MJ!) > > cheers > Bruce > > > On Mon, 15 Jan 2018, Aaron Tanenbaum wrote: > > Is the warp saved anywhere and where can I find it? Also is the warp > compatible > with FNIRT in any > way. I am interested in combining warps together to reduce the > number of > re-sampling steps. > Thank you so much in advanced > On Mon, Jan 15, 2018 at 8:53 AM, Bruce Fischl < > fis...@nmr.mgh.harvard.edu> wrote: > in the last stage there is a nonlinear atlas alignment that is > specific to > each timepoint. We are working on building a nonlinear base, > but it is not > distributed yet. > > cheers > Bruce > On Sun, 14 Jan 2018, Aaron > Tanenbaum wrote: > > > > > I am interested in knowing what type of alignment goes into > the last stage > of the > longitudinal > > pipeline. Are each longitudinal time point non-linearly > aligned to the base > image? If > so can I find > > the warp? > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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