Thank you both again for your reply. Right now, I am calculating ALFF and comparing it to functional connectivity.
Global intensity normalization is probably a good processing step for ALFF, but I had hoped to also look at ALFF without any sort of intensity normalization. >From what you are saying though, it sounds like this might be more effort than >its worth… Best, Erik > On Apr 11, 2018, at 6:45 PM, Harms, Michael <[email protected]> wrote: > > > We consider those “intermediate” files and thus they aren’t part of our > released packages or “CinaBox” disks. So, this could be rather challenging. > You would need to use “REST” calls into the ConnectomDB database directly to > pull down the files for each run. > > Perhaps you could describe why you need this scaling factor, and we can see > if we have any further insight. > > 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: [email protected] > <mailto:[email protected]> > > From: "Glasser, Matthew" <[email protected]> > Date: Wednesday, April 11, 2018 at 5:35 PM > To: erik lee <[email protected]>, "Harms, Michael" <[email protected]> > Cc: "[email protected]" <[email protected]> > 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: > > 1) ${StudyFolder}/${Subject}/${fMRIName}/BiasField.2.nii.gz > 2) ${StudyFolder}/${Subject}/${fMRIName}/rfMRI_REST1_LR_nonlin.nii.gz > 3) ${StudyFolder}/${Subject}/${fMRIName}/rfMRI_REST1_LR_nonlin_norm.nii.gz > > I expect you will find the normalization factor will be correlated with head > size and be related to the amount of coil loading each subject has. > > Keep in mind the same normalization factor was applied to all voxels. > > Matt. > > From: erik lee <[email protected] <mailto:[email protected]>> > Date: Wednesday, April 11, 2018 at 5:05 PM > To: "Harms, Michael" <[email protected] <mailto:[email protected]>> > Cc: Matt Glasser <[email protected] <mailto:[email protected]>>, > "[email protected] <mailto:[email protected]>" > <[email protected] <mailto:[email protected]>> > 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 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 <[email protected] >> <mailto:[email protected]>> 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: [email protected] >> <mailto:[email protected]> >> >> On 4/11/18, 2:31 PM, "[email protected] >> <mailto:[email protected]> on behalf of Glasser, >> Matthew" <[email protected] >> <mailto:[email protected]> on behalf of >> [email protected] <mailto:[email protected]>> 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, "[email protected] >> <mailto:[email protected]> on behalf of >> erik lee" <[email protected] >> <mailto:[email protected]> on behalf of >> [email protected] <mailto:[email protected]>> 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 >> >[email protected] <mailto:[email protected]> >> >http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> ><http://lists.humanconnectome.org/mailman/listinfo/hcp-users> >> >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] <mailto:[email protected]> >> 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. > > > > > 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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
