[HCP-Users] HCP script for freesurfer

Hi HCP team, I downloaded HCP script and I’m using that for anatomy image preprocessing and running FREESURFER. But, I received errors in one of steps in recon-all. I analyzed 111 individual subjects' T1 data using same method, but there are errors in only 14 subjects… I asked the error to

Re: [HCP-Users] mean intensity for FIX-denoised 7T data

Ah okay; remeaning as you suggested works well (restores the expected Tmean/Tsd). Thanks! From: Glasser, Matthew [glass...@wustl.edu] Sent: Tuesday, February 21, 2017 8:40 PM To: Ely, Benjamin; HCP-Users@humanconnectome.org Cc: Brown, Tim Subject: Re: [HCP-Users]

Re: [HCP-Users] mean intensity for FIX-denoised 7T data

Ugg, I thought we fixed that. You can take the mean image from the uncleaned data and add it to the cleaned data to have the mean present if you need it for some reason. Remember if you are concatenating across scans you will need to have the data demeaned. Peace, Matt. From:

Re: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline Differences Across Releases

Okay good to know. Thank you Matt. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) On Tue, Feb 21, 2017 at 4:28 PM, Glasser, Matthew wrote: > I think it is okay to over write for those

Re: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline Differences Across Releases

I think it is okay to over write for those pipelines. For the structural pipelines you cannot rerun FreeSurfer after running PostFreeSurfer. Matt. From: Timothy Hendrickson > Date: Tuesday, February 21, 2017 at 4:26 PM To: Matt Glasser

Re: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline Differences Across Releases

Darn. Alright I will reprocess the fMRI and DTI data. It sounds like the structural pipeline has not been changed so I would not have to reprocess that right? I am curious are the pipelines associated with the fMRI and DTI data smart enough to overwrite data files or do I have to totally delete

Re: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline Differences Across Releases

I had a look over this and there are some important changes for fMRIVolume (change in the way bias field correction is done) and potentially also some changes in the diffusion pipeline. While it would probably work fine, I would recommend rerunning if it isn’t too painful. Peace, Matt.

[HCP-Users] mean intensity for FIX-denoised 7T data

Hi HCP team, The FIX-denoised 7T data released by the HCP appear to have a mean intensity of ~0, versus 10,000 for the pre-FIX 7T data due to intensity normalization. By contrast, the most recently released 3T data from the HCP retain a mean value of ~10,000 following the ICA-FIX step. Is this

Re: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline Differences Across Releases

I’ll respond to this when I have a bit more info. Peace, Matt. From: > on behalf of Timothy Hendrickson > Date: Tuesday, February 21, 2017 at 11:07 AM To: "Harms,

Re: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline Differences Across Releases

I can see that several changes/additions have been made to 3.21, but I asked whether there is a difference in *just* the minimal preprocessing pipelines (i.e. PreFreeSurfer, FreeSurfer, PostFreeSurfer, fMRIVolume, fMRISurface, and Diffusion) between 3.4.0 and 3.21. I can ask this a different way,

Re: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline Differences Across Releases

There have been a lot of changes/additions from 3.4.0 to 3.21. If you are starting a new study, it would be preferable for you to start with the latest version. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience

Re: [HCP-Users] Comparing ICA-FIX results to results without ICA-FIX

Hi Andrew, To be clear, ICA-FIX may not improve task fMRI data when it is run separately on each tfMRI scan. MELODIC separates signal from noise better when there are tons of time points going into the ICA, which isn’t always the case with single tfMRI scans. Also, the confound regression will

[HCP-Users] Variation in HCP Minimal Preprocessing Pipeline Differences Across Releases

Hello, I have been using version 3.4.0 of the HCP Minimal Preprocessing Pipeline to process my HCP compatible data. I've used 3.4.0 to run the structural (PreFreeSurfer, FreeSurfer, PostFreeSurfer), fMRI (fMRIVolume, and fMRISurface), and diffusion sub-pipelines. I have now downloaded version