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Initial edit for freesurfer 7's tkregister change #176

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Initial edit for freesurfer 7's tkregister change #176

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fb11c98
Initial edit for freesurfer 7's tkregister change
coalsont May 5, 2020
ecf8cac
Simpler possible solution to tkregister FS7 issue
coalsont May 6, 2020
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10 changes: 5 additions & 5 deletions FreeSurfer/FreeSurferPipeline.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -75,8 +75,8 @@ show_tool_versions()

# Show tkregister version
log_Msg "Showing tkregister version"
which tkregister
tkregister -version
which tkregister2_cmdl
tkregister2_cmdl -version

# Show mri_concatenate_lta version
log_Msg "Showing mri_concatenate_lta version"
Expand Down Expand Up @@ -778,7 +778,7 @@ main()
fi

log_Msg "...Create a registration between the original conformed space and the rawavg space"
tkregister_cmd="tkregister"
tkregister_cmd="tkregister2_cmdl"
tkregister_cmd+=" --mov orig.mgz"
tkregister_cmd+=" --targ rawavg.mgz"
tkregister_cmd+=" --regheader"
Expand Down Expand Up @@ -811,7 +811,7 @@ main()
fi

log_Msg "...Convert to FSL format"
tkregister_cmd="tkregister"
tkregister_cmd="tkregister2_cmdl"
tkregister_cmd+=" --mov orig/${t2_or_flair}raw.mgz"
tkregister_cmd+=" --targ rawavg.mgz"
tkregister_cmd+=" --reg Q.lta"
Expand Down Expand Up @@ -847,7 +847,7 @@ main()
# Note that the convention of tkregister2 is that the resulting $reg is the registration
# matrix that maps from the "--targ" space into the "--mov" space.

tkregister2 --mov ${mridir}/rawavg.mgz --targ ${mridir}/orig.mgz --noedit --regheader --reg $reg
"tkregister2_cmdl" --mov ${mridir}/rawavg.mgz --targ ${mridir}/orig.mgz --noedit --regheader --reg $reg

#The ?h.white.deformed surfaces are used in FreeSurfer BBR registrations for fMRI and diffusion and have been moved into the HCP's T1w space so that BBR produces a transformation containing only the minor adjustment to the registration.
mri_surf2surf --s ${SubjectID} --sval-xyz white --reg $reg --tval-xyz ${mridir}/rawavg.mgz --tval white.deformed --surfreg white --hemi lh
Expand Down