Input Data for HCP Pipelines

[raia...@gmail.com]

Hi,

We are using the Lifespan HCP-Development and HCP-Aging Siemens Prisma protocol package to acquire our scans. For the T1 and T2 images, the scanner produces two sets of image for each.

T1:

1. "ImageType": "ORIGINAL", "PRIMARY", "M", "ND"

2. "ImageType": "ORIGINAL", "PRIMARY", "M", "ND", "NORMALIZED"

T2:

1. "ImageType": "ORIGINAL", "PRIMARY", "M", "ND"

2. "ImageType": "ORIGINAL", "PRIMARY", "M", "ND", "NORMALIZED", "SH", "FIL"

I am new to neuroimaging processing and was wondering when we input data into the three FreeSurfer pipelines, do we input both scans for each sequence? Or do we only input the scans that are not normalized? I am just a little confused because I think I read somewhere that only raw data is supposed to be used, so I just wanted to confirm which scans are okay to input. I know the pipeline can detect multiple scans, I just don't know whether all of them have to be non normalized.

Best,

Aikam Rai

[Glasser, Matthew]

Going forward it is better to use pre-scan normalize on all scans (T1w, T2w, fMRI, dMRI, SE Fieldmap, ASL).

Matt.

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[Harms, Michael]

 

To expand a little bit, the protocol was set up to generate Prescan Normalized (“NORMALIZED”) and non-normalized recons for the T1w and T2w scans. You would only use one of each as structural scan inputs to the HCPpipelines.

 

As Matt said, if you are just starting your data acquisitions, and don’t have any particular need to match the HCP-LS protocol exactly, our current suggestion would be that you turn on Prescan Normalize for all the other scan types, and then use the Prescan Normalized data from all modalities.

 

If that isn’t an option (e.g., data acquisition is far along, or already done), I’d use the recons *without* NORMALIZED as your structural scan inputs.

 

Cheers,

-MH

 

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Michael Harms, Ph.D.

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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

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[Glasser, Matthew]

I agree with that. 

Matt.

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[Aikam Rai]

Thank you so much! Additionally, when I was running the first pipeline it requires gradunwarp. On the usage and installation instructions, it says we require version 1.1.0 of the package. However, when you open the gradunwarp GitHub page, I believe it say that the HCP version of the pipelines is version 1.2.3. I am using the newer version at the moment, but I just wanted to confirm which package you wanted us to use because the installation page was updated quite recently and so I am not sure if the requirements actually changed or not?

Best,

Aikam 

[Glasser, Matthew]

I have changed it to 1.2.3 or later.

 

Matt.

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