In addition to making the template change to 0.8mm, the following variables need to be set appropriately: TE=“NONE” DwellTime SEUnwarpDir T1wSampleSpacing T2wSampleSpacing
The information needed to set these will hopefully be somewhere on these webpages: http://protocols.humanconnectome.org/ http://lifespan.humanconnectome.org/ I don’t know enough about which lifespan data you are attempting to process to know where the info is more specifically, but perhaps someone else on the list does. Peace, Matt. From: wtj <1257735...@qq.com<mailto:1257735...@qq.com>> Date: Tuesday, March 28, 2017 at 10:17 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Subject: 答复: 答复: 答复: 答复: [HCP-Users] brainmask.mgz Hi, I see. First, there are 8 templates to use in prefreesurfer. The lifespan data has a structural parameter “0.8mm isotropic”. So I need to change number 0.7 to 0.8 in T1wTemplate, T1wTemplateBrain, T2wTemplate, T2wTemplateBrain and TemplateMask, right? Second, to change the value of T1wSampleSpacing and T2wSampleSpacing(Is this what you mean?) according to my data, where should I find proper value of them? Thanks. 发件人: Glasser, Matthew [mailto:glass...@wustl.edu] 发送时间: 2017年3月28日 21:23 收件人: wtj <1257735...@qq.com<mailto:1257735...@qq.com>>; HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 主题: Re: 答复: 答复: 答复: [HCP-Users] brainmask.mgz 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 <1257735...@qq.com<mailto:1257735...@qq.com>> Date: Tuesday, March 28, 2017 at 8:17 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> 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:glass...@wustl.edu] 发送时间: 2017年3月28日 20:47 收件人: wtj <1257735...@qq.com<mailto:1257735...@qq.com>>; HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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 <1257735...@qq.com<mailto:1257735...@qq.com>> Date: Tuesday, March 28, 2017 at 7:37 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> 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:glass...@wustl.edu] 发送时间: 2017年3月28日 17:29 收件人: wtj <1257735...@qq.com<mailto:1257735...@qq.com>>; HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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 <1257735...@qq.com<mailto:1257735...@qq.com>> Date: Monday, March 27, 2017 at 11:30 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> 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:glass...@wustl.edu] 发送时间: 2017年3月27日 22:31 收件人: wtj <1257735...@qq.com<mailto:1257735...@qq.com>>; HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 主题: Re: [HCP-Users] brainmask.mgz What version of FreeSurfer are you using and do you have enough disk space? Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of wtj <1257735...@qq.com<mailto:1257735...@qq.com>> Date: Monday, March 27, 2017 at 8:03 AM To: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" <HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>> 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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If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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