Re: [HCP-Users] Issue about new FreeSurferPipeline

2019-03-20 Thread Glasser, Matthew
How did you call the FreeSurfer pipeline? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Qunjun Liang mailto:liangqun...@foxmail.com>> Date: Wednesday, March 20, 2019 at 10:07 PM To: "hcp-users@humanconnectome.org" mailto:hcp-user

[HCP-Users] Issue about new FreeSurferPipeline

2019-03-20 Thread Qunjun Liang
Dear experts, Environment: HCP Pipeline v4.0.0, FreeSurfer v6.0.0, Ubuntu 14.04 I recently used the FreeSurfer pipeline to preprocess my data while an error came out. FreeSueferPipeline.sh: ABORTING: unrecognized option: --printcom= But when I have switched the pipeline utility to FreeSurfe

Re: [HCP-Users] PostFreesurfer possible bug

2019-03-20 Thread Harms, Michael
Your --subjectDIR flag isn’t set correctly. Take a look at Examples/Scripts/FreeSurferPipelineBatch.sh for how FreeSurferPipeline.sh should be called. (Or modify the StudyFolder, Subjlist, and EnvironmentScript entries in Examples/Scripts/FreeSurferPipelineBatch.sh script and use that to actu

Re: [HCP-Users] PostFreesurfer possible bug

2019-03-20 Thread Harms, Michael
No idea. Are you using a modified/customized version of the HCPpipelines? Which exact version are you using? What is your exact call to FreeSurferPipeline.sh? Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Was

Re: [HCP-Users] PostFreesurfer possible bug

2019-03-20 Thread Shachar Gal
well, for some reason, when i run the piplines it gets created under the subject directory this is the ls for my subject directory drwxr-x--- 3 shachar Users 4096 Mar 19 16:24 unprocessed drwxr-xr-x 6 rootroot 4096 Mar 20 10:47 T2w drwxrwxr-x 10 rootroot 4096 Mar 20 11:46 102 lrwxrwxrwx

Re: [HCP-Users] PostFreesurfer possible bug

2019-03-20 Thread Harms, Michael
Hi, The FreeSurferFolder is located at $StudyFolder/$Subject/T1w/$Subject, which is what PostFreeSurferPipeline.sh is setting up via the following combination of lines: FreeSurferFolder="$Subject" #L101 T1wFolder="$StudyFolder"/"$Subject"/"$T1wFolder" #L137 FreeSurferFolder="$T1wFolder"/"$Fre

[HCP-Users] PostFreesurfer possible bug

2019-03-20 Thread Shachar Gal
Dear experts, in the PostFreeSurferPipeline script, the FreeSurferFolder is set to be "$T1wFolder"/"$FreeSurferFolder" even though, the free surfer folder isnt actually under the T1w folder... its right inside the subject's directory (WorkingDirectory/SubjectNumber/SubjectNumber) is this a bug, o