Re: [HCP-Users] ICA failure with volumetric ICA-FIX denoised files

2017-03-28 Thread Glasser, Matthew
Indeed melodic is a single threaded application that takes quite some time to run the PCA portion of the ICA, even on the CIFTI data. Hopefully one day it will be multi-threaded. I think you would have to use fewer subjects or a matlab-based MIGP (this is what I use). You can actually run

Re: [HCP-Users] 答复: 答复: 答复: 答复: brainmask.mgz

2017-03-28 Thread Glasser, Matthew
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/

Re: [HCP-Users] ICA failure with volumetric ICA-FIX denoised files

2017-03-28 Thread Stephen Smith
Hi - I would strongly recommend doing the group-ICA and dualregression on the CIFTI versions of the data, not volumetric. However, if you really want volumetric versions of 50-dimensional group-ICA then we could provide those that have been done via group-ICA on CIFTI data which has then been

Re: [HCP-Users] ICA failure with volumetric ICA-FIX denoised files

2017-03-28 Thread Jenny Gilbert
Hi Matt, I appreciate your help with working through ICA using HCP data. Following your recommendation, I converted CIFTI files to NIFTI and am trying to run through ICA, but I am still experiencing problems. Running ICA for 62 participants (rest1_RL session) on a high power computing server

Re: [HCP-Users] 答复: 答复: 答复: brainmask.mgz

2017-03-28 Thread Glasser, Matthew
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

Re: [HCP-Users] 答复: 答复: brainmask.mgz

2017-03-28 Thread Glasser, Matthew
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> Date: Tuesday, March 28, 2017 at 7:37 AM To: Matt

Re: [HCP-Users] 答复: brainmask.mgz

2017-03-28 Thread Glasser, Matthew
How did you call the FreeSurfer pipeline and did you run PreFreeSurfer first? Peace, Matt. From: wtj <1257735...@qq.com> Date: Monday, March 27, 2017 at 11:30 PM To: Matt Glasser > Subject: 答复: [HCP-Users] brainmask.mgz