Hi, You could also fork the repository and integrate the changes -- hopefully it will show up in the main release.
Do you mind sending me your altered version of the Pipelines? I would like to inspect the differences in code. I notice you have a few posts regarding the pipelines today. Regards, _______________________________________ Bryan Chiu Undergraduate Research Assistant Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy Faculty of Medicine University of British Columbia ________________________________________ From: [email protected] [[email protected]] on behalf of [email protected] [[email protected]] Sent: Tuesday, June 16, 2015 10:00 AM To: [email protected] Subject: HCP-Users Digest, Vol 31, Issue 12 Send HCP-Users mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit http://lists.humanconnectome.org/mailman/listinfo/hcp-users or, via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of HCP-Users digest..." Today's Topics: 1. BedpostX and Diffusion Processing Pipeline (Chiu, Bryan (PHTH)) 2. netcdf libs (m s) 3. inf loop bug in scripts (m s) 4. -openmp option issue (m s) ---------------------------------------------------------------------- Message: 1 Date: Mon, 15 Jun 2015 20:23:47 +0000 From: "Chiu, Bryan (PHTH)" <[email protected]> Subject: [HCP-Users] BedpostX and Diffusion Processing Pipeline To: "[email protected]" <[email protected]> Message-ID: <680d9b8d5feaaf40a1a5878265424ca49e312...@s-itsv-mbx06p.ead.ubc.ca> Content-Type: text/plain; charset="iso-8859-1" Hi, I am aware that processed Diffusion data is coming up in an upcoming data release. I was looking for the processing pipeline that is being used on the HCP (featuring bedpostX, probtrackX) but could not find it on Github. Is there an ETA on the release of this pipeline? I would like to use it on my existing DTI data to see how closely I represent my data with respect to the HCP. Kind Regards, _______________________________________ Bryan Chiu Undergraduate Research Assistant Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy Faculty of Medicine University of British Columbia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20150615/1d2affd6/attachment-0001.html ------------------------------ Message: 2 Date: Tue, 16 Jun 2015 11:53:06 -0400 From: m s <[email protected]> Subject: [HCP-Users] netcdf libs To: [email protected] Message-ID: <canboeglbwqgcjs40mkp0wpeecbmplkpyepm6mdnjkev72vm...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Version 3.4.0 Hi, I've been installing HCP Pipelines 3.4.0. Thanks for the great software, the research teams here at Penn are excited to use it! We've had some issues that I thought I'd post in different threads. This one's about netcdf libs. You might consider listing netcdf libs as a prereq for the required HCP version of freesurfer. The mris_make_surfaces tools needs libnetcdf.so.6 from netcdf-4.1.1-3.el6.5. -Michael -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20150616/1472eef0/attachment-0001.html ------------------------------ Message: 3 Date: Tue, 16 Jun 2015 12:22:18 -0400 From: m s <[email protected]> Subject: [HCP-Users] inf loop bug in scripts To: [email protected] Message-ID: <canboegkrfuh8cgvu3h1ghxkxsgz_abmr6urpnv___rumexj...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Version 3.4.0 Hi, A number of the scripts in Example/Scripts fail to recognize malformed arguments and get stuck in an infinite loop, e.g. PreFreeSurferPipelineBatch.sh. A couple scripts handle this correctly, e.g. generate_level1_fsf.sh. -M -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20150616/cd86fb29/attachment-0001.html ------------------------------ Message: 4 Date: Tue, 16 Jun 2015 12:24:04 -0400 From: m s <[email protected]> Subject: [HCP-Users] -openmp option issue To: [email protected] Message-ID: <CANBOeg+57PmFXr=haqz_0yfuddg7zhyzzpc07nszu6m_zwj...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Version 3.4.0 Hi, The Pipelines-3.4.0//FreeSurfer/FreeSurferPipeline.sh script has a hard-coded value of 8 for the -openmp argument in the call to recon-all. This doesn't seem like a good idea. Seems it should be an option and default to 1. We've modified it to work with NSLOTS for SGE on our cluster. Here's the diff if you're interested: < cp "$SubjectDIR"/"$SubjectID"/mri/brainmask.auto.mgz "$SubjectDIR"/"$SubjectID"/mri/brainmask.mgz < < # CFN mod - use $NSLOTS to define multithreading < if [[ -z "$NSLOTS" ]]; then < NSLOTS=1 < fi < < recon-all -subjid $SubjectID -sd $SubjectDIR -autorecon2 -nosmooth2 -noinflate2 -nocurvstats -nosegstats -openmp $NSLOTS --- > cp "$SubjectDIR"/"$SubjectID"/mri/brainmask.auto.mgz "$SubjectDIR"/"$SubjectID"/mri/brainmask.mgz > recon-all -subjid $SubjectID -sd $SubjectDIR -autorecon2 -nosmooth2 -noinflate2 -nocurvstats -nosegstats -openmp 8 -------------- next part -------------- An HTML attachment was scrubbed... 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