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 wasn’t exactly sure what the file names would be for the following: 1. Input rfMRI (pre-Jacobian/Bias Field correction) 2. Bias Image 3. Jacobian Image 4. Output rfMRI (post-Jacobian/Bias Field correction and global intensity normalization, but before any temporal processing) Presumably once I have these, I could do some simple algebra at any given voxel to find the global mean used in the intensity normalization. Thanks, Erik > On Apr 11, 2018, at 3:43 PM, Harms, Michael <mha...@wustl.edu> wrote: > > > 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 > GenericfMRIVolumeProcessingPipeline.sh > > 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. > > Cheers, > -MH > > -- > 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 > <mailto:mha...@wustl.edu> > > On 4/11/18, 2:31 PM, "hcp-users-boun...@humanconnectome.org > <mailto:hcp-users-boun...@humanconnectome.org> on behalf of Glasser, Matthew" > <hcp-users-boun...@humanconnectome.org > <mailto:hcp-users-boun...@humanconnectome.org> on behalf of > glass...@wustl.edu <mailto: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 > files. > > Peace, > > Matt. > > On 4/11/18, 2:21 PM, "hcp-users-boun...@humanconnectome.org > <mailto:hcp-users-boun...@humanconnectome.org> on behalf of > erik lee" <hcp-users-boun...@humanconnectome.org > <mailto:hcp-users-boun...@humanconnectome.org> on behalf of > erik.lee...@gmail.com <mailto: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 > >brain? > > > >(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! > > > >Best, > >Erik Lee > >_______________________________________________ > >HCP-Users mailing list > >HCP-Users@humanconnectome.org > >http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> > > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
