[HCP-Users] A question about 164k data

Dear HCP experts, I have a question about 164k data. Is there a computational less expensive way to calculate MSMAll-registered 164k individual myelin maps from the existing data? There were only MSMAll-registered 164k myelin maps with bias field corrected there in the existing data, but I am

Re: [HCP-Users] Extracting beta values from analyzed task-data

And, to answer the Q in your 1st paragraph: yes. BTW: Since you want the “betas", you should use the pe1.dtseries.nii files. But, as an aside, note that these pe’s/cope’s are the results of the Level2 analysis, essentially averaging the Level 1 (individual runs). Because all the contrasts

Re: [HCP-Users] Extracting beta values from analyzed task-data

Grand mean 1. Find out what SPM uses and adjust your internal scale accordingly... Peace, Matt. From: Vadim Axelrod Sent: Monday, October 17, 2016 1:41:35 PM To: Harms, Michael Cc: Glasser, Matthew; hcp-users@humanconnectome.org

Re: [HCP-Users] Extracting beta values from analyzed task-data

Thank you for the help! So, if I want to get a beta estimate for the condition, I should take pe image in the cope#.feat folder, where this condition is compared vs. fixation. For example, in the Language task, for the Math beta I should take pe image in cope1.feat (MATH-fixation) and the Story

Re: [HCP-Users] hcp_fix bug

Is this compiled matlab or not compiled? Peace, Matt. From: > on behalf of nailin yao > Date: Monday, October 17, 2016 at 11:13 AM To:

Re: [HCP-Users] gradunwarp - "array index out of bounds" error in coef_file_parse routine

That is the correct fix for this problem. It has no side-effects. Some scanners (eg: Siemens 7T) have coefficients of even higher orders, so you can actually increase the siemens_cas to 100 or so to accommodate the full range. That value just determines the preallocation, and the matrix is

[HCP-Users] hcp_fix bug

Hi , I received the bug report when running hcp_fix for the last step: running FIX FIX Feature extraction for Melodic output directory: rfMRI_REST1_LR_nonlin_norm_hp2000.ica create edge masks run FAST registration of standard space masks extract features FIX Classifying components in

Re: [HCP-Users] Extracting beta values from analyzed task-data

No, in the updated pipeline, we simply have some code to merge the copes/betas from the different contrasts into a single file for each task (as we did for the zstat maps, which perhaps somewhat confusingly, are the files named as _tfMRI__level2_hp200_s?.dscalar.nii or

Re: [HCP-Users] Extracting beta values from analyzed task-data

Thank you, Matt. So, you mean that in the updated pipeline cope1.dtseries.nii contains multiple beta maps (two or more, depending on a contrast)? Practically, do you think in the foreseeable future there will be an update of task data for the download, that will include the betas? If not, then I

Re: [HCP-Users] Extracting beta values from analyzed task-data

It looks like the released HCP task fMRI data were produced using an older version of the Task analysis pipeline that does not automatically collate the beta maps into a labeled and easy to use dscalar file. The beta maps will be in these files: