Did PreFreeSurfer complete successfully? It doesn’t look like you modified PreFreeSurfer to account for the 0.8mm resolution of the lifespan data or the differing readout sample spacing among other things. You need to make sure that all of the acquisition parameters that the pipeline requires are appropriately set for the data you are processing.
Peace, Matt. From: wtj <[email protected]<mailto:[email protected]>> Date: Tuesday, March 28, 2017 at 8:17 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: 答复: 答复: 答复: [HCP-Users] brainmask.mgz Hi, https://github.com/Washington-University/Pipelines/wiki/v3.4.0-Release-Notes,-Installation,-and-Usage#prerequisites I did what the links told me to do. I just changed batch scripts, not pipelines themselves. In attachments you could see where have I changed. Is there something wrong? Thanks. 发件人: Glasser, Matthew [mailto:[email protected]] 发送时间: 2017年3月28日 20:47 收件人: wtj <[email protected]<mailto:[email protected]>>; [email protected]<mailto:[email protected]> 主题: Re: 答复: 答复: [HCP-Users] brainmask.mgz Did you change the pipelines themselves or the scripts that call the pipelines? Please post the arguments used to call both the PreFreeSurfer and FreeSurfer pipelines. Peace, Matt. From: wtj <[email protected]<mailto:[email protected]>> Date: Tuesday, March 28, 2017 at 7:37 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: 答复: 答复: [HCP-Users] brainmask.mgz Hi, I know that freesurfer pipeline use prefreesurfer pipeline’s output as input. There are three more folders under every subject’s folder, T1w, T2w, and MNINonLinear after prefreesurfer part. I called FreeSurferPipelineBatch.sh in ../Pipelines-3.22.0-beta.5/Examples/Scripts after changing something to adapt to new data. Besides, there are some main changes in prefreesurfer part. My data use Spin Echo Field Maps, not Siemens specific Gradient Echo Field Maps. However, freesurfer part have all inputs that it need provided by prefreesurfer part. So, why not just create the new folder and files? Why it stopped? Thanks. 发件人: Glasser, Matthew [mailto:[email protected]] 发送时间: 2017年3月28日 17:29 收件人: wtj <[email protected]<mailto:[email protected]>>; [email protected]<mailto:[email protected]> 主题: Re: 答复: [HCP-Users] brainmask.mgz How did you call the FreeSurfer pipeline and did you run PreFreeSurfer first? Peace, Matt. From: wtj <[email protected]<mailto:[email protected]>> Date: Monday, March 27, 2017 at 11:30 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: 答复: [HCP-Users] brainmask.mgz Hi， There are 69.5GB left in my studyfolder directory at present. Isn’t that enough? My freesurfer version is 5.3.0-HCP. There are 27 donors’ data. Each of them occupies about 2.5GB space, how much more space is needed before freesurfer part of pipeline? Thanks. 发件人: Glasser, Matthew [mailto:[email protected]] 发送时间: 2017年3月27日 22:31 收件人: wtj <[email protected]<mailto:[email protected]>>; [email protected]<mailto:[email protected]> 主题: Re: [HCP-Users] brainmask.mgz What version of FreeSurfer are you using and do you have enough disk space? Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of wtj <[email protected]<mailto:[email protected]>> Date: Monday, March 27, 2017 at 8:03 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] brainmask.mgz Hi, I ran the pipeline on example data well, but when I did the freesurferpipeline part on WU-Minn HCP Lifespan Pilot Data, it stopped and report an error: ERROR: failure writing /home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2009/T1w/LS2009/mri/brainmask.mgz and in *.e.7443,it reported, mghWrite(/home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2009/T1w/LS2009/mri/brainmask.mgz, -1): could not open file The detail is in attachment. I compared the output log file with one of example data, everything seems fine before something went wrong. Can you help me? 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