Re: [HCP-Users] HCP scan protocols for Siemens prisma scanner request

Hi, At this point in time, see here: http://protocols.humanconnectome.org/CCF/ What we are using for the HCP-Aging/Development projects for fMRI and dMRI differs in only very minor (probably inconsequential) aspects relative to what is available via the web page above. We hope to get the exact

Re: [HCP-Users] comparison across acquisitions

thanks :) On Thu, Apr 27, 2017 at 3:01 PM, Harms, Michael wrote: > > That means that the collection of their fMRI spanned the date of the > change in the recon algorithm, so some was reconned with the “r177” > algorithm, and some with the “r227” algorithm. > > cheers, > -MH >

Re: [HCP-Users] Question about the CCA calculation from "A positive-negative mode of population covariation links ..."

Hi - here's some additional code - I *think* this is the relevant code for what you're asking about. Cheers. % temporary version of vars, useful for various null tests below grotvars=inormal(vars); grotvars(:,std(grotvars)<1e-10)=[]; grotvars(:,sum(isnan(grotvars)==0)<20)=[]; % permutation

Re: [HCP-Users] Fwd: Using multiple cores while running Structural Pipelines

The fMRIVolume pipeline also takes advantage of SGE through fslsub, and we hacked it to use condor as well--that allows for significant time savings on our end _ gaurav patel gauravpa...@gmail.com www.neurofreak.net > On Apr 27, 2017, at 2:29 PM, Glasser, Matthew

[HCP-Users] Question about the CCA calculation from "A positive-negative mode of population covariation links ..."

Hi HCP group, I have a question regarding how to compute the variance explained after running CCA on the HCP data using the code from http://www.fmrib.ox.ac.uk /datasets/HCP-CCA/. I ran it on the 461 subject subset with dimensionality reduced to 100 dimensions. The result from the code is very

Re: [HCP-Users] comparison across acquisitions

I think that means that one session was with one recon and the other with another recon. Peace, Matt. From: Joelle Zimmermann > Date: Thursday, April 27, 2017 at 1:50 PM To: Matt Glasser

Re: [HCP-Users] comparison across acquisitions

One more question about this - a few subjects have: r177 r227 for the fMRI recon. Does this mean both were done? Which of the two was used for these subjects for the S900 release? Thanks, Joelle On Wed, Apr 26, 2017 at 2:05 PM, Glasser, Matthew wrote: > Yes. > > Peace, >

Re: [HCP-Users] Fwd: Using multiple cores while running Structural Pipelines

Hi Mike, The only thing that is parallelized in the minimal preprocessing pipelines aside from specific FreeSurfer binaries is wb_command. wb_command defaults to using as many cores as the system has. More advanced pipelines that use matlab will adhere to matlab¹s parallelization behaviors.

[HCP-Users] HCP scan protocols for Siemens prisma scanner request

Hi, I will use this protocol for a new study. The scan protocol seems to be implemented at our scanner already, but I just want to make sure all parameters are identical when citing you. Would you please send me the scan protocols for the Siemens 3T Prisma scanner? Best regards, Franziska

[HCP-Users] Last weeks to register for HCP Course 2017

It's not too late to register for the 2017 HCP Course: "Exploring the Human

Re: [HCP-Users] Fwd: Using multiple cores while running Structural Pipelines

Matt, Tim, What is parallelized in the fMRI pipelines? I would be good if we created a FAQ entry on the HCP Wiki detailing: (1) Which aspects of the pipelines are parallelized and the default number of cores used for each. (2) Which wb_commands are parallelized and the default number of cores

Re: [HCP-Users] Fwd: Using multiple cores while running Structural Pipelines

For what its worth, on our workstations we run each subject's anatomy pipeline as a separate thread, which takes 8-12 hours, then use the parallelization to speed up the fMRI pipelines with either SGE/OGE or ht_condor, with a thread devoted to each bold run being processed

Re: [HCP-Users] [SPAM] Re: [SPAM] Re: [TaskfMRILevel2]feat_model error

Perhaps you can paste in how you are calling the TaskfMRIAnalysis pipeline (not the run local part but rather what is in that script). Peace, Matt. From: -- <744652...@qq.com> Date: Thursday, April 27, 2017 at 8:48 AM To: Matt Glasser

Re: [HCP-Users] [SPAM] Re: [TaskfMRILevel2]feat_model error

The data and the Pipeline scripts are all included in the 2015 HCP Course, and the subject ID is 100307. Besides, I have already running three structural pipelines and two functional pipelines. Best, Bai Haohao -- Original -- From: "Glasser,

Re: [HCP-Users] Fwd: Using multiple cores while running Structural Pipelines

The number of windows you use to launch the processing is irrelevant. But if you only have 8 cores on your machine, and only want to use 7 of them, you can’t run 50 subjects at once. In this case, where you have a bunch of subjects to process, I would run 7 subjects at a time, while limiting

Re: [HCP-Users] [SPAM] Re: [TaskfMRILevel2]feat_model error

Are you using HCP data or your own task fMRI data? Peace, Matt. From: -- <744652...@qq.com> Date: Thursday, April 27, 2017 at 3:56 AM To: Matt Glasser >, hcp-users

[HCP-Users] Fwd: Using multiple cores while running Structural Pipelines

Alright, thanks! And just for clarification for dummies: if not installing something like grid_engine, will running all 50 subjects in one Terminal window or 10 subjects in each of five different windows be more efficient? Or doesn't it make any difference? And I estimate around 20 days for 50

Re: [HCP-Users] [TaskfMRILevel2]feat_model error

Hello, I modify the TaskfMRIAnalysisBatch.sh to change StudyFolder, Subjlist and EnvironmentScript to my own file path. Then I write a bash file to call copy_evs_into_results.sh and generate_level1_fsf.sh to generate the files. Followed Day4_Practical7_Task_fMRI tutorial, I install