Re: [Freesurfer] Longitudinal Pipeline (fwd)

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 fischl@nmr.mgh.harvard.edu wrote:

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}_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 <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? > > _______________________________________________ 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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