Re: [HCP-Users] How to do cluster-level correction on the raw T statistical cifti data

2016-12-01 Thread Glasser, Matthew
We recommend the PALM software package in FSL for this sort of thing: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM Peace, Matt. From: > on behalf of Cai Yue >

[HCP-Users] How to do cluster-level correction on the raw T statistical cifti data

2016-12-01 Thread Cai Yue
Dear HCP developers, I have a problem with the cluster-level correction on the cifti data. I have searched a lot on the internet about this issue, but haven't got solutions. I got the p and T cifti data from the GLM analysis. I am wonderting if there is a cluster-level method (like alphasim)

Re: [HCP-Users] Exporting the dense connectome matrix

2016-12-01 Thread Glasser, Matthew
The file you are requesting would exceed 200GB in size and as a result we don't support this (the equivalent CIFTI file is 32.5GB). If you are having specific issues with analyzing CIFTI files, let us know what those are and we can help. Peace, Matt. From:

[HCP-Users] Exporting the dense connectome matrix

2016-12-01 Thread Dayan, Eran
Hi all, I was wondering if there is an easy way to export the dense functional connectome matrix into a txt file? I am specifically interested in the voxel by voxel matrix, rather than the grayordinate matrix. Tried to download the relevant cifti file from DB and open it in MATLAB (using a

Re: [HCP-Users] Distorted MNI space result (T?w_restore) -- maybe due to "bad" initial brain mask?

2016-12-01 Thread Harms, Michael
Note that the scenes we’ve assembled for “StructuralQC” include a check of the FNIRT registration. You can find the scripts necessary to generate those scenes here: https://github.com/Washington-University/StructuralQC cheers, -MH -- Michael Harms, Ph.D.

Re: [HCP-Users] Gradient power amplifier error

2016-12-01 Thread Harms, Michael
Hi, Re (1): I believe you need a license to run in FREE mode. Do you have it? Re (2): By how much was it clipped? You could try reducing the flip angles — 78/160 is what we’ve been using for HCP. Or, increase the duration of the relevant pulse on the Sequence:Special tab. Re (3): I see that

Re: [HCP-Users] Gradient power amplifier error

2016-12-01 Thread Harms, Michael
BTW, Re (2): We are Excite/Refocus Pulse durations of 3840/7680 in our 1.5 mm protocol currently. -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of

Re: [HCP-Users] BOLD sequence does not run

2016-12-01 Thread Harms, Michael
Your Excite Pulse Duration on the Sequence:Special tab is much too low. We’ve been using 6600 microsec for HCP. Offline recon on a Skyra would require that you set up the “remote recon server”. If that isn’t set up, you’ll need to use “Online” recon. cheers, -MH -- Michael Harms, Ph.D.