I don’t see the error message there. Peace,
Matt. From: Nicolo Biagi <n.bi...@pgr.reading.ac.uk<mailto:n.bi...@pgr.reading.ac.uk>> Date: Wednesday, August 2, 2017 at 5:52 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] Problems with the HCP Pipeline Hi Matt, Thank you for your reply. I managed to install and set up all the software you mentioned. I was also able to run the Pre-FreeSurfer processing without any problems. I tried then to run the FreeSurfer processing on my terminal. Before running the script FreeSurferPipelineBatch.sh I've edited it and changed the StudyFolder, Subjlist and EnvironmentScript variables and then run it, but I got the following message: Nicos-MacBook-Pro:Scripts nico$ ./FreeSurferPipelineBatch.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 /Users/nico/projects/Pipelines-master/FreeSurfer/FreeSurferPipeline.sh set -- --subject=100307 --subjectDIR=/Users/nico/projects/projects/Pipelines_ExampleData/100307/T1w --t1=/Users/nico/projects/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_restore.nii.gz --t1brain=/Users/nico/projects/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_restore_brain.nii.gz --t2=/Users/nico/projects/projects/Pipelines_ExampleData/100307/T1w/T2w_acpc_dc_restore.nii.gz --printcom= . /Users/nico/projects/Pipelines-master/Examples/Scripts/SetUpHCPPipeline.sh Do you know why I got this message and how can I fix it? Thank you for your time. Best, Nicolò Biagi PhD Student School of Psychology and Clinical Language Sciences University of Reading ________________________________ From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: 28 July 2017 13:02:39 To: Nicolo Biagi; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>; Brown, Tim Subject: Re: [HCP-Users] Problems with the HCP Pipeline I would start with the latest version of the HCP Pipelines, FSL, and Connectome Workbench (and FreeSurfer version 5.3). You also will need to make sure that FSL is properly sourced in your environment. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Nicolo Biagi <n.bi...@pgr.reading.ac.uk<mailto:n.bi...@pgr.reading.ac.uk>> Date: Friday, July 28, 2017 at 4:21 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "Brown, Tim" <tbbr...@wustl.edu<mailto:tbbr...@wustl.edu>> Subject: [HCP-Users] Problems with the HCP Pipeline Hi, I am currently trying to set up the HCP Pipeline on my MacBook Pro, but I'm having a hard time even if I'm following the instructions here https://github.com/Washington-University/Pipelines/wiki/v3.4.0-Release-Notes,-Installation,-and-Usage. First I couldn't find the FSL 5.0.6 and so I've installed the FSL 5.0.10, do you know where I can find the correct version? After I edited the PreFreeSurferPipelineBatch.sh with the correct directories for the StudyFolder, Subjlist, and the EnvironmentScript, I've tried to execute the batch but the message I get in my Terminal is the following: StudyFolder: /Users/nico/projects/projects/Pipelines_ExampleData Subjlist: 100307 EnvironmentScript: /Users/nico/projects/Pipelines-master/Examples/Scripts/SetUpHCPPipeline.sh Run locally: This script must be SOURCED to correctly setup the environment prior to running any of the other HCP scripts contained here 100307 Found 1 T1w Images for subject 100307 Found 1 T2w Images for subject 100307 About to use fsl_sub to queue or run //Users/nico/projects/PreFreeSurfer/PreFreeSurferPipeline.sh The command you have requested cannot be found or is not executable Do you know what I'm doing wrong? Thank you for your help. Best regards, Nicolò Biagi PhD Student School of Psychology and Clinical Language Sciences University of Reading _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
