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.

https://github.com/Washington-University/NHPPipelines/blob/cb237b1b5b01e4bdf764f6615ea7e0a0c2c2bea9/FreeSurfer/FreeSurferPipelineNHP.sh#L312-L319

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.