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Washington-University / HCPpipelines

Processing pipelines for the HCP
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issues with postFreesurfer script #169

Closed rosella1234 closed 4 years ago

rosella1234 commented 4 years ago

Running this script gives the following error: biolab@rocco:~/HCP/HCPpipelines-3.19.0/Examples/Scripts$ ./PostFreeSurferPipelineBatch.sh This script must be SOURCED to correctly setup the environment prior to running any of the other HCP scripts contained here

100307 About to use fsl_sub to queue or run /home/biolab/HCP/HCPpipelines-3.19.0/PostFreeSurfer/PostFreeSurferPipeline.sh mghRead(/home/biolab/HCP/100307/T1w/100307/mri/brain.finalsurfs.mgz, -1): could not open file mghRead(/home/biolab/HCP/100307/T1w/100307/mri/brain.finalsurfs.mgz, -1): could not open file mghRead(/home/biolab/HCP/100307/T1w/100307/mri/brain.finalsurfs.mgz, -1): could not open file Image Exception : #63 :: No image files match: /home/biolab/HCP/100307/T1w/wmparc_1mm terminate called after throwing an instance of 'std::runtime_error' what(): No image files match: /home/biolab/HCP/100307/T1w/wmparc_1mm /home/biolab/HCP/HCPpipelines-3.19.0/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh: line 80: 29885 Aborted fslmaths "$T1wFolder"/wmparc_1mm.nii.gz -bin -dilD -dilD -dilD -ero -ero "$T1wFolder"/"$T1wImageBrainMask"_1mm.nii.gz set -- --path=/home/biolab/HCP --subject=100307 --surfatlasdir=/home/biolab/HCP/HCPpipelines-3.19.0/global/templates/standard_mesh_atlases --grayordinatesdir=/home/biolab/HCP/HCPpipelines-3.19.0/global/templates/91282_Greyordinates --grayordinatesres=2 --hiresmesh=164 --lowresmesh=32 --subcortgraylabels=/home/biolab/HCP/HCPpipelines-3.19.0/global/config/FreeSurferSubcorticalLabelTableLut.txt --freesurferlabels=/home/biolab/HCP/HCPpipelines-3.19.0/global/config/FreeSurferAllLut.txt --refmyelinmaps=/home/biolab/HCP/HCPpipelines-3.19.0/global/templates/standard_mesh_atlases/Conte69.MyelinMap_BC.164k_fs_LR.dscalar.nii --regname=FS --printcom= . /home/biolab/HCP/HCPpipelines-3.19.0/Examples/Scripts/SetUpHCPPipeline.sh

glasserm commented 4 years ago

Better to ask these questions on the HCP-Users mailing list. When you post there, please note if you successfully ran PreFreeSurfer and FreeSurfer pipelines.