Re: [HCP-Users] Question about unprocessed fMRI data

Hi Ben, Yes, the CMRR multiband sequence incorporates "dynamic off-resonance in k-space” (DORK)” method as in Pfeuffer et al., MRM 2002, which has already been implemented in the Siemens product EPI sequence ICE recon. Gordon > On Jun 8, 2017, at 12:05 PM, Benjamin Risk

Re: [HCP-Users] Question about unprocessed fMRI data

I see, thank you! On Thu, Jun 8, 2017 at 3:08 PM, Glasser, Matthew wrote: > I suppose it isn’t good enough given what we see in some subjects FD > traces however… > > Matt. > > From: on behalf of "Harms, > Michael" >

Re: [HCP-Users] values in myelin maps

I’m happy to hear that! Peace, Matt. From: Lisa Kramarenko > Date: Thursday, June 8, 2017 at 2:18 PM To: "Harms, Michael" > Cc: Matt Glasser >,

Re: [HCP-Users] values in myelin maps

thanks so much, it works and myelin maps look good now! Lisa On 8 June 2017 at 16:15, Harms, Michael wrote: > > ‘mkdir’ is telling you that the directory already exists. Normally that > won’t abort a script, but it does in this case because of the “set -e” at > the top of

Re: [HCP-Users] Question about unprocessed fMRI data

I suppose it isn’t good enough given what we see in some subjects FD traces however… Matt. From: > on behalf of "Harms, Michael" > Date: Thursday, June 8, 2017 at 2:05

Re: [HCP-Users] Question about unprocessed fMRI data

This is via Essa: It is the same as what is done in the Siemens product - these are Siemens code/algorithms. But yes - they do B0 corrections, including in post-processing. -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of

Re: [HCP-Users] [HCP-Info] [Contact Form]: Transforming Group MPM Parcellations to fsaverage

The parcellation file is available here: https://balsa.wustl.edu/file/show/3VLx Note that the preferred venue for asking questions about HCP data is the HCP-Users mailing list so that all list members have the benefit of the answer. Peace, Matt. From:

[HCP-Users] Question about unprocessed fMRI data

Dear HCP experts, I am trying to better understand the unprocessed fMRI data. Does the online reconstruction include corrections for spatial shifts due to B0 fluctuations? There is a note about this in Ugurbil et al 2013 but I am wondering if this applies to the final HCP acquisition protocol.

Re: [HCP-Users] Matching field map resolutions to images

Hi Mike, That is for spin echo field maps. Matt. From: "Harms, Michael" > Date: Thursday, June 8, 2017 at 9:26 AM To: Matt Glasser >, Grant Sutcliffe >,

Re: [HCP-Users] Matching field map resolutions to images

In theory, the resolutions and matrix size don’t need to match. But I thought that, as a practical matter, the Pipelines don’t work if they don’t match. At least that was the case at some point in the past... -- Michael Harms, Ph.D. ---

Re: [HCP-Users] values in myelin maps

‘mkdir’ is telling you that the directory already exists. Normally that won’t abort a script, but it does in this case because of the “set -e” at the top of the script. The easy solution is to add the -p flag to the mkdir command, so that it is no longer considered an error if the directory

Re: [HCP-Users] values in myelin maps

You could delete that or make the mkdir a conditional if it doesn’t already exist. Peace, Matt. From: Lisa Kramarenko > Date: Thursday, June 8, 2017 at 4:21 AM To: Matt Glasser > Cc:

Re: [HCP-Users] Matching field map resolutions to images

What is most important is that they both cover the whole brain for gradient echo field maps. Matching geometry more exactly is nice but not necessary. Peace, Matt. From: > on behalf of Grant Sutcliffe

[HCP-Users] Matching field map resolutions to images

Hi, just to check, for the preprocessing pipelines, is it necessary or advisable to match the resolutions between field map images and the images to be corrected? Specifically I am interested in the case of gradient echo field maps and fMRI timeseries. Regards, Grant

Re: [HCP-Users] values in myelin maps

I am sorry, I have made a mistake in the mail above. It seems that the Pipeline ended in the end of the "FreeSurferHiresPial.sh" script and not the Intermediate recon-all steps. It ended after Reading surface file /Users/user/Desktop/003/T1w/ 003/surf/rh.pial.postT2.pass2 Applying linear

Re: [HCP-Users] values in myelin maps

I wasn't sure about the exact hacking process and just naively commented out lines 133-167 in the FreeSurfer script, so that I started with recon-all -subjid $SubjectID -sd $SubjectDIR -autorecon2 -nosmooth2 -noinflate2 -nocurvstats -nosegstats -openmp ${num_cores} ${seed_cmd_appendix} (with