uot; <mha...@wustl.edu<mailto:mha...@wustl.edu>>
Cc: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org&
e...@gmail.com>, "Harms, Michael" <mha...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] Grand Mean Intensity Normalization
>
> Jacobian wasn’t used for the 3T fMRI data. Also the bias field
lt;mha...@wustl.edu>
Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Grand Mean Intensity Normalization
Jacobian wasn’t used for the 3T fMRI data. Also the bias field correction was
non-optimal. These are the files that you would want:
<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Grand Mean Intensity Normalization
Hi Matt and Michael,
Thank you both for your helpful replies.
If I wanted to back-calculate the original mean
Hi Matt and Michael,
Thank you both for your helpful replies.
If I wanted to back-calculate the original mean of the rfMRI image after bias
field and Jacobian correction, do you know what the appropriate files would be
to do this?
Looking at the HCP data/intensity normalization script, I
Just to expand on this, since I think I might know why you are asking.
The grand mean is computed on the brain masked volume timeseries, after bias
field correction and jacobian modulation is first applied – see the end of
IntensityNormalization.sh, which is called as the final step in
1) The overall mean of each scan is 1, this is not done voxelwise
(e.g. like a bias correction would be).
2) Unfortunately this information is not saved. I don¹t think fslmaths
outputs it, perhaps it could be back computed from some intermediate
files.
Peace,
Matt.
On 4/11/18, 2:21 PM,
Dear HCP Experts,
I am currently using the temporally preprocessed rfMRI data in the S900 release
(aka rfMRI_REST?_??_Atlas_hp2000_clean.dtseries.nii).
According to the Smith 2013 NeuroImage paper, it sounds like the images I am
using have all received global intensity normalization prior to
