[RESOLVED] Parcellate_anat: error in calculating surface

miemiemiaomiaotu · December 3, 2025, 6:28am

Hi, all

When I use function ‘parcellate_anat’ to calculate corrThickness、curvature、surface、MyelinMap_BC, only calculating ‘surface’ exists an error in all sessions. failed to open file '/mnt/ssd2/qzheng/STG_GroupLevel/qunex/STG_GroupLevel/sessions/STG022/hcp/STG022/MNINonLinear/fsaverage_LR32k/STG022.surface.32k_fs_LR.dscalar.nii', file does not exist, or folder permissions prevent seeing it

After checking files, I really can’t find xx.surface.32k_fs_LR.dscalar.nii in fsaverage_LR32k folder. I want to know which step generated this file xx.surface.32k_fs_LR.dscalar.nii. Did I lose some essential steps？

My command is as follows:

parcellate_anat_surf)

    qunex_container parcellate_anat \\

        --sessionsfolder="${WORK_DIR}/${STUDY_NAME}/sessions" \\

        --sessions="${SUBJ}" \\

        --extractdata="yes" \\

        --parcellationfile="${WORK_DIR}/Schaefer2018_400Parcels_17Networks_order.dlabel.nii" \\

        --inputdatatype="surface" \\

        --outname="parcellate_surface" \\

        --overwrite="no"\\

        --bind="${SDIR}:${SDIR}"  \\

        --container="${QUNEX_CONTAINER}";

Here is my log file

error_parcellate_anat_STG022_2025-12-03_10.31.52.142648.log (2.7 KB)

Thanks for kindly help!

Best, Kelly

demsarjure · December 3, 2025, 8:12am

Hi Kelly,

There is no surface file. What file gets parcellated is defined with the inputdatatype parameter. This is where the surface comes from. Here, you need to be more specific (MyelinMap_BC, corrThickness…).

Best, Jure

miemiemiaomiaotu · December 3, 2025, 8:44am

Hi Jure,

I found that I am not sure which file should be used to calculate surface area. Below are the file names in my fsaverage_LR32k folder. Could you help me check which one should be used to calculate surface area?

STG026.32k_fs_LR.wb.spec
STG026.aparc.32k_fs_LR.dlabel.nii
STG026.aparc.a2009s.32k_fs_LR.dlabel.nii
STG026.ArealDistortion.32k_fs_LR_parcellate_surface.csv
STG026.ArealDistortion_FS.32k_fs_LR.dscalar.nii
STG026.ArealDistortion_MSMAll.32k_fs_LR.dscalar.nii
STG026.ArealDistortion_MSMAll_InitialReg_1_d40_WRN.32k_fs_LR.dscalar.nii
STG026.ArealDistortion_MSMAll_InitialReg_2_d40_WRN.32k_fs_LR.dscalar.nii
STG026.ArealDistortion_MSMSulc.32k_fs_LR.dscalar.nii
STG026.atlas_MyelinMap_BC.32k_fs_LR.dscalar.nii
STG026.atlas_RSNs_d40.32k_fs_LR.dscalar.nii
STG026.atlas_Topographic_ROIs.32k_fs_LR.dscalar.nii
STG026.atlas_Topography.32k_fs_LR.dscalar.nii
STG026.BiasField_MSMAll.32k_fs_LR.dscalar.nii
STG026.BiasField_MSMAll_InitialReg_1_d40_WRN.32k_fs_LR.dscalar.nii
STG026.BiasField_MSMAll_InitialReg_2_d40_WRN.32k_fs_LR.dscalar.nii
STG026.BiasField_MSMSulc.32k_fs_LR.dscalar.nii
STG026.corrThickness.32k_fs_LR.dscalar.nii
STG026.corrThickness.32k_fs_LR_parcellate_anat.csv
STG026.corrThickness.32k_fs_LR_parcellate_anat.pscalar.nii
STG026.corrThickness.32k_fs_LR_parcellate_corrThickness.csv
STG026.corrThickness.32k_fs_LR_parcellate_corrThickness.pscalar.nii
STG026.corrThickness_MSMAll.32k_fs_LR.dscalar.nii
STG026.curvature.32k_fs_LR.dscalar.nii
STG026.curvature.32k_fs_LR_parcellate_anat.csv
STG026.curvature.32k_fs_LR_parcellate_anat.pscalar.nii
STG026.curvature.32k_fs_LR_parcellate_curvature.csv
STG026.curvature.32k_fs_LR_parcellate_curvature.pscalar.nii
STG026.curvature_MSMAll.32k_fs_LR.dscalar.nii
STG026.EdgeDistortion_FS.32k_fs_LR.dscalar.nii
STG026.EdgeDistortion_MSMAll.32k_fs_LR.dscalar.nii
STG026.EdgeDistortion_MSMAll_InitialReg_2_d40_WRN.32k_fs_LR.dscalar.nii
STG026.EdgeDistortion_MSMSulc.32k_fs_LR.dscalar.nii
STG026.fs.32k_fs_LR_parcellate_anat.csv
STG026.individual_RSNs_d40_MSMAll_InitialReg_1_d40_WRN.32k_fs_LR.dscalar.nii
STG026.individual_RSNs_d40_MSMAll_InitialReg_2_d40_WRN.32k_fs_LR.dscalar.nii
STG026.individual_RSNs_d40_MSMSulc.32k_fs_LR.dscalar.nii
STG026.individual_RSNs_d40_weights.32k_fs_LR.dscalar.nii
STG026.individual_Topography_MSMAll_InitialReg_1_d40_WRN.32k_fs_LR.dscalar.nii
STG026.individual_Topography_MSMAll_InitialReg_2_d40_WRN.32k_fs_LR.dscalar.nii
STG026.individual_Topography_weights.32k_fs_LR.dscalar.nii
STG026.L.aparc.32k_fs_LR.label.gii
STG026.L.aparc.a2009s.32k_fs_LR.label.gii
STG026.L.ArealDistortion_FS.32k_fs_LR.shape.gii
STG026.L.ArealDistortion_MSMSulc.32k_fs_LR.shape.gii
STG026.L.atlas_MyelinMap_BC.32k_fs_LR.func.gii
STG026.L.atlasroi.32k_fs_LR.shape.gii
STG026.L.atlasroi_inv.32k_fs_LR.shape.gii
STG026.L.atlas_RSNs_d40.32k_fs_LR.func.gii
STG026.L.atlas_Topography.32k_fs_LR.func.gii
STG026.L.BiasField_MSMAll_InitialReg_1_d40_WRN.32k_fs_LR.func.gii
STG026.L.BiasField_MSMSulc.32k_fs_LR.func.gii
STG026.L.corrThickness.32k_fs_LR.shape.gii
STG026.L.curvature.32k_fs_LR.shape.gii
STG026.L.EdgeDistortion_FS.32k_fs_LR.shape.gii
STG026.L.EdgeDistortion_MSMSulc.32k_fs_LR.shape.gii
STG026.L.flat.32k_fs_LR.surf.gii
STG026.L.individual_RSNs_d40_MSMAll_InitialReg_1_d40_WRN.32k_fs_LR.func.gii
STG026.L.individual_RSNs_d40_MSMSulc.32k_fs_LR.func.gii
STG026.L.individual_RSNs_d40_weights.32k_fs_LR.func.gii
STG026.L.individual_Topography_MSMAll_InitialReg_1_d40_WRN.32k_fs_LR.func.gii
STG026.L.individual_Topography_weights.32k_fs_LR.func.gii
STG026.L.inflated.32k_fs_LR.surf.gii
STG026.L.inflated_MSMAll.32k_fs_LR.surf.gii
STG026.L.midthickness.32k_fs_LR.surf.gii
STG026.L.midthickness_MSMAll.32k_fs_LR.surf.gii
STG026.L.Modalities_1.32k_fs_LR.func.gii
STG026.L.Modalities_1_weights.32k_fs_LR.func.gii
STG026.L.Modalities_2.32k_fs_LR.func.gii
STG026.L.Modalities_2_weights.32k_fs_LR.func.gii
STG026.L.MyelinMap.32k_fs_LR.func.gii
STG026.L.MyelinMap_BC.32k_fs_LR.func.gii
STG026.L.norm_atlas_MyelinMap_BC.32k_fs_LR.func.gii
STG026.L.norm_atlas_RSNs_d40.32k_fs_LR.func.gii
STG026.L.norm_atlas_Topography.32k_fs_LR.func.gii
STG026.L.norm_MyelinMap_BC.32k_fs_LR.func.gii
STG026.L.pial.32k_fs_LR.surf.gii
STG026.L.pial_MSMAll.32k_fs_LR.surf.gii
STG026.L.SmoothedMyelinMap.32k_fs_LR.func.gii
STG026.L.SmoothedMyelinMap_BC.32k_fs_LR.func.gii
STG026.L.sphere.32k_fs_LR.surf.gii
STG026.L.sphere.MSMAll_InitialReg_1_d40_WRN.32k_fs_LR.surf.gii
STG026.L.sphere.MSMAll_InitialReg_2_d40_WRN.32k_fs_LR.surf.gii
STG026.L.sphere.MSMSulc.32k_fs_LR.surf.gii
STG026.L.StrainJ_FS.32k_fs_LR.shape.gii
STG026.L.StrainJ_MSMSulc.32k_fs_LR.shape.gii
STG026.L.StrainR_FS.32k_fs_LR.shape.gii
STG026.L.StrainR_MSMSulc.32k_fs_LR.shape.gii
STG026.L.sulc.32k_fs_LR.shape.gii
STG026.L.thickness.32k_fs_LR.shape.gii
STG026.L.very_inflated.32k_fs_LR.surf.gii
STG026.L.very_inflated_MSMAll.32k_fs_LR.surf.gii
STG026.L.white.32k_fs_LR.surf.gii
STG026.L.white_MSMAll.32k_fs_LR.surf.gii
STG026.MSMAll.32k_fs_LR.wb.spec
STG026.MyelinMap.32k_fs_LR.dscalar.nii
STG026.MyelinMap_BC.32k_fs_LR.dscalar.nii
STG026.MyelinMap_BC.32k_fs_LR_parcellate_myelin.csv
STG026.MyelinMap_BC.32k_fs_LR_parcellate_myelin.pscalar.nii
STG026.MyelinMap_BC_MSMAll.32k_fs_LR.dscalar.nii
STG026.MyelinMap_BC_MSMAll_InitialReg_2_d40_WRN.32k_fs_LR.dscalar.nii
STG026.MyelinMap_MSMAll.32k_fs_LR.dscalar.nii
STG026.MyelinMap_MSMAll_InitialReg_1_d40_WRN.32k_fs_LR.dscalar.nii
STG026.MyelinMap_MSMAll_InitialReg_2_d40_WRN.32k_fs_LR.dscalar.nii
STG026.R.aparc.32k_fs_LR.label.gii
STG026.R.aparc.a2009s.32k_fs_LR.label.gii
STG026.R.ArealDistortion_FS.32k_fs_LR.shape.gii
STG026.R.ArealDistortion_MSMSulc.32k_fs_LR.shape.gii
STG026.R.atlas_MyelinMap_BC.32k_fs_LR.func.gii
STG026.R.atlasroi.32k_fs_LR.shape.gii
STG026.R.atlasroi_inv.32k_fs_LR.shape.gii
STG026.R.atlas_RSNs_d40.32k_fs_LR.func.gii
STG026.R.atlas_Topography.32k_fs_LR.func.gii
STG026.R.BiasField_MSMAll_InitialReg_1_d40_WRN.32k_fs_LR.func.gii
STG026.R.BiasField_MSMSulc.32k_fs_LR.func.gii
STG026.R.corrThickness.32k_fs_LR.shape.gii
STG026.R.curvature.32k_fs_LR.shape.gii
STG026.R.EdgeDistortion_FS.32k_fs_LR.shape.gii
STG026.R.EdgeDistortion_MSMSulc.32k_fs_LR.shape.gii
STG026.RefMyelinMap.32k_fs_LR.dscalar.nii
STG026.R.flat.32k_fs_LR.surf.gii
STG026.R.individual_RSNs_d40_MSMAll_InitialReg_1_d40_WRN.32k_fs_LR.func.gii
STG026.R.individual_RSNs_d40_MSMSulc.32k_fs_LR.func.gii
STG026.R.individual_RSNs_d40_weights.32k_fs_LR.func.gii
STG026.R.individual_Topography_MSMAll_InitialReg_1_d40_WRN.32k_fs_LR.func.gii
STG026.R.individual_Topography_weights.32k_fs_LR.func.gii
STG026.R.inflated.32k_fs_LR.surf.gii
STG026.R.inflated_MSMAll.32k_fs_LR.surf.gii
STG026.R.midthickness.32k_fs_LR.surf.gii
STG026.R.midthickness_MSMAll.32k_fs_LR.surf.gii
STG026.R.Modalities_1.32k_fs_LR.func.gii
STG026.R.Modalities_1_weights.32k_fs_LR.func.gii
STG026.R.Modalities_2.32k_fs_LR.func.gii
STG026.R.Modalities_2_weights.32k_fs_LR.func.gii
STG026.R.MyelinMap.32k_fs_LR.func.gii
STG026.R.MyelinMap_BC.32k_fs_LR.func.gii
STG026.R.norm_atlas_MyelinMap_BC.32k_fs_LR.func.gii
STG026.R.norm_atlas_RSNs_d40.32k_fs_LR.func.gii
STG026.R.norm_atlas_Topography.32k_fs_LR.func.gii
STG026.R.norm_MyelinMap_BC.32k_fs_LR.func.gii
STG026.R.pial.32k_fs_LR.surf.gii
STG026.R.pial_MSMAll.32k_fs_LR.surf.gii
STG026.R.SmoothedMyelinMap.32k_fs_LR.func.gii
STG026.R.SmoothedMyelinMap_BC.32k_fs_LR.func.gii
STG026.R.sphere.32k_fs_LR.surf.gii
STG026.R.sphere.MSMAll_InitialReg_1_d40_WRN.32k_fs_LR.surf.gii
STG026.R.sphere.MSMAll_InitialReg_2_d40_WRN.32k_fs_LR.surf.gii
STG026.R.sphere.MSMSulc.32k_fs_LR.surf.gii
STG026.R.StrainJ_FS.32k_fs_LR.shape.gii
STG026.R.StrainJ_MSMSulc.32k_fs_LR.shape.gii
STG026.R.StrainR_FS.32k_fs_LR.shape.gii
STG026.R.StrainR_MSMSulc.32k_fs_LR.shape.gii
STG026.R.sulc.32k_fs_LR.shape.gii
STG026.R.thickness.32k_fs_LR.shape.gii
STG026.R.very_inflated.32k_fs_LR.surf.gii
STG026.R.very_inflated_MSMAll.32k_fs_LR.surf.gii
STG026.R.white.32k_fs_LR.surf.gii
STG026.R.white_MSMAll.32k_fs_LR.surf.gii
STG026.SmoothedMyelinMap.32k_fs_LR.dscalar.nii
STG026.SmoothedMyelinMap_BC.32k_fs_LR.dscalar.nii
STG026.SmoothedMyelinMap_BC_MSMAll.32k_fs_LR.dscalar.nii
STG026.SphericalDistortion_MSMAll.32k_fs_LR.dscalar.nii
STG026.SphericalDistortion_MSMAll_InitialReg_2_d40_WRN.32k_fs_LR.dscalar.nii
STG026.StrainJ_FS.32k_fs_LR.dscalar.nii
STG026.StrainJ_MSMAll.32k_fs_LR.dscalar.nii
STG026.StrainJ_MSMAll_InitialReg_2_d40_WRN.32k_fs_LR.dscalar.nii
STG026.StrainJ_MSMSulc.32k_fs_LR.dscalar.nii
STG026.StrainR_FS.32k_fs_LR.dscalar.nii
STG026.StrainR_MSMAll.32k_fs_LR.dscalar.nii
STG026.StrainR_MSMAll_InitialReg_2_d40_WRN.32k_fs_LR.dscalar.nii
STG026.StrainR_MSMSulc.32k_fs_LR.dscalar.nii
STG026.sulc.32k_fs_LR.dscalar.nii
STG026.sulc.32k_fs_LR_parcellate_surface.csv
STG026.sulc.32k_fs_LR_parcellate_surface.pscalar.nii
STG026.sulc_MSMAll.32k_fs_LR.dscalar.nii
STG026.sulc_MSMAll_InitialReg_2_d40_WRN.32k_fs_LR.dscalar.nii
STG026.surface.32k_fs_LR_parcellate_anat.csv
STG026.surface.32k_fs_LR_parcellate_surface.csv
STG026.thickness.32k_fs_LR.dscalar.nii
STG026.thickness_MSMAll.32k_fs_LR.dscalar.nii

Many thanks for your kindly help!

Best, Kelly

demsarjure · December 3, 2025, 9:28am

I believe thickness is for cortical thickness, while midthickness is for cortical surface area. I am not 100% sure though. Maybe best to check on the HCP users group (https://groups.google.com/a/humanconnectome.org/g/hcp-users).

Best, Jure

miemiemiaomiaotu · December 4, 2025, 4:18am

Hi, Jure

After checking on the HCP users group, I have found the correct file for calculating cortical surface area.

Thanks so much for your kindly help!!

Best, Kelly