In FreeSurferPipelineNHP.sh "Image Exception : #63 :: No image files match: global/templates/MacaqueYerkes19/wmskeleton.nii.gz"

[TakJim]

@takuya-hayashi

I am testing the operation of NHPPipelines, and I need MacaqueYerkes19/wmskeleton.nii.gz for the following part of the runNormalize2 () process in FreeSurferPipelineNHP.sh.

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

Is it possible for you to share the necessary files with us?

By the way, GCAdir is set in SetUpHCPPipelineNHP.sh as follows.

export GCAdir="${HCPPIPEDIR_Templates}/MacaqueYerkes19" #Template Dir with FreeSurfer NHP GCA and TIF files

[YCHuang0610]

https://github.com/Washington-University/NHPPipelines/pull/3/files
According to the pull requeset: Structural pipelines updates #3 update in 2020 by Takuya Hayahsi, the wmskeleton.nii.gz was from the ./global/templates/MacaqueRIKEN21 directory. The template folder composition was different in that version from now. So I think, maybe you can simply copy this file to ./global/templates/MacaqueYerkes19/ or set the GCAdir to MacaqueRIKEN21.