FYI

---------- Forwarded message ----------
Date: Tue, 16 Jan 2018 19:59:38 +0000
From: Mark Jenkinson <mark.jenkinson@ndcn.ox.ac.uk>
To: Bruce Fischl <fischl@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}_warp_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 <fischl@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 <fischl@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?
           >
           >
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The information in this e-mail is intended only for the person to whom it is
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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
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