Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance?

No, we were proposing this: M = cifti map of mean(of Level 2 individual subject copes) S = cifti map of std(of Level 2 individual subject copes) Cohen’s d = M/S cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of

Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance?

I think this would be done from a level3 file; maybe I'm wrong. If I understand this correctly, the three steps below would give a Cohen's d map. Have I understood it right?: 1st) take this file: HCP_S900_787_tfMRI_ALLTASKS_level3_zstat1_hp200_s2_MSMAll.dscalar.nii 2nd) transform this file into

Re: [HCP-Users] is workbench command only available for Linux, not Windows?

Workbench is available for Linux, Windows, and Mac: http://www.humanconnectome.org/software/get-connectome-workbench.html It is also open source, so if you want it in some other OS type where QT compiles, you can try compiling it yourself: https://github.com/Washington-University/workbench The

Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance?

Hi Matthew, I am sorry, I didn't fully understand your previous message. Do you mean that the two steps that I mentioned in my last message are correct? Thank you very much, Xavier. From: Glasser, Matthew [glass...@wustl.edu] Sent: Monday, January 30, 2017 7:22 PM

[HCP-Users] is workbench command only available for Linux, not Windows?

Hi, I am a very new user of the workbench. I noticed the availability of the Workbench Command and went to its home page. The example there shows Operating System: Linux. Is it not available for WindowsOS? Is it for MacOS? Thanks, -Jeff ___

Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance?

Those are the level 2 copes. Peace, Matt. From: Xavier Guell Paradis > Date: Monday, January 30, 2017 at 6:20 PM To: Matt Glasser >, "Harms, Michael" >, "Elam,

Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance?

No because the non-optimal scaling will divide out in the mean(cope)/std(cope) ratio. Peace, Matt. From: Xavier Guell Paradis > Date: Monday, January 30, 2017 at 4:35 PM To: "Harms, Michael" >, "Elam,

Re: [HCP-Users] How to know cluster size (number of voxels) after -cifti-find-clusters

The -cifti-find-clusters command assigns a separate integer within each cluster. You can use -cifti-label-import and then -cifti-all-labels-to-rois to get each cluster in a separate map. Then, -cifti-weighted-stats with -spatial-weights and -sum will give you mm^2 for surface clusters and mm^3

Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance?

Dear Michael, Wouldn't using the cope files have the problem that "the released versions are not optimally scaled (because of a non-optimal intensity bias field correction)" (as written by Matthew before in this conversation)? Or would this not matter if Cohen's d were calculated from cope1

Re: [HCP-Users] Running bedpostx on HCP diffusion data

Hi Moises, Thanks for the reply! I also want to know a couple other things - is Sun Grid Engine (SGE) a particular requirement to ensure bedpostx internally splits the slices among all available CPU cores? Or will something like Torque and Maui also be fine? The system administrator in my

[HCP-Users] How to know cluster size (number of voxels) after -cifti-find-clusters

Dear HCP experts, After using -cifti-find-clusters, is there a way to know the size of the clusters that the command has found? We know that the clusters will be larger than the specified volume-value-threshold, but is there a way to know the mm^3 or number of voxels of the clusters identified?

Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance?

Dear Michael and Matthew, Thank you very much for all your replies, your comments were extremely helpful. Xavier. From: Harms, Michael [mha...@wustl.edu] Sent: Monday, January 30, 2017 12:30 PM To: Elam, Jennifer; Glasser, Matthew; Xavier Guell Paradis;