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




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