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 
glass...@wustl.edu> wrote:

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

erik.lee...@gmail.com> wrote:

>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

>temporal preprocessing.


>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!



>Erik Lee


>HCP-Users mailing list




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