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
There is NOT another grand mean normalization applied specifically to the CIFTI
data, so don’t expect the CIFTI data to have a grand mean of 10000. IIRC, the
grand mean of the CIFTI timeseries tends to end up in the 8000-9000 range.
Michael Harms, Ph.D.
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
On 4/11/18, 2:31 PM, "hcp-users-boun...@humanconnectome.org on behalf of
Glasser, Matthew" <hcp-users-boun...@humanconnectome.org on behalf of
1) The overall mean of each scan is 10000, 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
On 4/11/18, 2:21 PM, "hcp-users-boun...@humanconnectome.org on behalf of
erik lee" <hcp-users-boun...@humanconnectome.org on behalf of
>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 the
>I have two sets of questions relating to this:
>(1) Does this mean that the global mean of all voxels (averaged across
>time points) is used to normalize each voxel? If this is the case, is
>this the mean of every voxel in the image, or exclusively those in the
>(2) Looking through ConnectomeDB, I couldn¹t find a file with the scaling
>factor used for normalizing. Is this something that is saved anywhere?
>Thanks for the help!
>HCP-Users mailing list
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