Dear HCP users, I am a beginner of HCP Pipelines, and I have installed necessary tools including freesurfer_v5.3.0_HCP, fsl_v5.0.9(I can not find v5.0.6), HCP Workbench, HCP Pipelines scripts and other dependencies. I have also downloaded HCP example data to test structural processing part of HCP Pipelines, fallowing the guidance here(https://github.com/Washington-University/Pipelines/wiki/v3.4.0-Release-Notes,-Installation,-and-Usage).
However, I encounter errors when it comes to the 3rd part of structural processing: Post-freesurfer-processing. I checked the automatically generated file named xxx.sh.exxxx, and found out that only a file named PostFreeSurferPipeline.sh.e6340 contains errors messages, which mean that nothing wrong with the first two part. The errors messages are : mghRead(/100307/T1w/100307/mri/brain.finalsurfs.mgz, -1): could not open file mghRead(/100307/T1w/100307/mri/brain.finalsurfs.mgz, -1): could not open file mghRead(/100307/T1w/100307/mri/brain.finalsurfs.mgz, -1): could not open file /home/yoson/Applications/HCP_Pipelines/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh: line 63: /100307/T1w/100307/mri/c_ras.mat: No such file or directory Nothing wrong with environment variables setting. I also have the privilege to read, write and execute all files. Your generous help would be greatly appreciated. Best regards, YC Yao _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users