wmskeleton.nii.gz for Marmosets

[ajallenunc]

Hello @takuya-hayashi,

I hope this message finds you well. I am currently engaged in a project involving the analysis of Marmoset data and came across a similar problem as reported in a previous issue #5 . It appears that I am missing the file MarmosetRIKEN/wmskeleton.nii.gz, which is needed in

NHPPipelines/FreeSurfer/FreeSurferPipelineNHP.sh

Lines 312 to 319 in cb237b1

	if [[ $SPECIES =~ Marmoset || $SPECIES =~ Macaque ]] ; then
	applywarp -i "$GCAdir"/wmskeleton.nii.gz -r ../../T1w_acpc_dc_restore.nii.gz -w \
	../../../MNINonLinear/xfms/standard2acpc_dc.nii.gz -o wmskeleton.nii.gz --interp=nn
	"$PipelineScripts"/MakeDimto1mm.sh Marmoset wmskeleton.nii.gz
	fslmaths wmskeleton_1mm.nii.gz -thr 0.2 -bin -mul 255 wmskeleton_1mm.nii.gz
	mri_convert -ns 1 -odt uchar wmskeleton_1mm.nii.gz wmskeleton_1mm_conform.nii.gz --conform
	fslmaths wmskeleton_1mm_conform.nii.gz -mul 110 -max wm.nii.gz wm.nii.gz
	fi

Would it be possible for you to add this file to the repository? Alternatively, if the file is available elsewhere, could you kindly direct me to the appropriate source?

Thanks

[takuya-hayashi]

Hi Adrian,
Sorry for not inlucding this file in this version of the pipelne. We are now working on the new version of the NHP-HCP pipeline. Attached is the latest version of the marmoset wmskeleton MarmosetRIKEN20_Averagewmskeleton.nii.gz
, which can be used in combinnation with MarmosetRIKEN20 templates:
https://balsa.wustl.edu/study/p005n