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: mha...@wustl.edu
From: "Glasser, Matthew" <glass...@wustl.edu>
Date: Wednesday, April 11, 2018 at 5:35 PM
To: erik lee <erik.lee...@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 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 <erik.lee...@gmail.com<mailto:erik.lee...@gmail.com>>
Date: Wednesday, April 11, 2018 at 5:05 PM
To: "Harms, Michael" <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>>
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
<mha...@wustl.edu<mailto: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<mailto:HCP-Users@humanconnectome.org>
>http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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