Hello all,
I am trying to align the cortical surfaces of my neonatal population (obtained using the minimal processing structural dHCP pipeline) to the surface template.
I’ve been trying to use the command lines obtained from @EmmaR github:
for hemi in L R; do
if [ "$hemi" == "L" ]; then inmesh=$native_rot_sphereL refmesh=$templatesphereL refdata=$templatedataL indata=$native_dataL outname=$outdir/surface_transforms/sub-${subjid}_ses-${session}_left_ else inmesh=$native_rot_sphereR refmesh=$templatesphereR indata=$native_dataR refdata=$templatedataR outname=$outdir/surface_transforms/sub-${subjid}_ses-${session}_right_ fi if [ ! -f ${outname}sphere.reg.surf.gii ]; then echo ${MSMBIN} --conf=${config} --inmesh=${inmesh} --refmesh=${refmesh} --indata=${indata} --refdata=${refdata} --out=${outname} --verbose ${MSMBIN} --conf=${config} --inmesh=${inmesh} --refmesh=${refmesh} --indata=${indata} --refdata=${refdata} --out=${outname} --verbose fi # need to concatenate msm warp to local template with warp from local template to 40 week template ${WB_BIN} -surface-sphere-project-unproject ${outname}sphere.reg.surf.gii ${refmesh} ${SURF2TEMPLATE}/dHCP_between_template_warps/${age}-to-40.MSMSulc.sphere.reg.surf.gii ${outname}sphere.reg40.surf.gii # the output sphere represents the full warp from Native to 40 week template space - save this cp ${outname}sphere.reg40.surf.gii ${topdir}/sub-${subjid}/ses-$session/anat/Native/
However, I don’t find the folder with the warps. Is this folder available? Or it is better just to skip this step and register the subjects directly to the 40 weeks template? Thanks in advance.
Best regards,
Manuel