To summarize the thread and some off-list conversations for future 
readers, it is the case that the HCP pipelines normalize the task fMRI 
images to the MNI atlas in volume space. This part of the preprocessing 
pipeline is different from the procedure used in Anticevic et al. 2008 
(doi:10.1016/j.neuroimage.2008.02.052), and was chosen for computational 
efficiency (since the subcortical data needs to be mapped to MNI volume 
space), and since the resolution costs were judged to be small.

These threads refer to similar issues:
http://www.mail-archive.com/hcp-users@humanconnectome.org/msg01323.html
http://www.mail-archive.com/hcp-users@humanconnectome.org/msg01234.html
http://www.mail-archive.com/hcp-users@humanconnectome.org/msg00356.html

thanks again Matt and Tim,
Jo


On 4/24/2015 11:56 AM, Glasser, Matthew wrote:
> I don’t really want to recapitulate my more detailed responses to this
> question previously on the list (why atlas register the fMRI data to MNI
> space in the volume vs to native subject space or even vs bringing the
> surfaces into the original EPI space).  The basics are that motion
> correction, distortion correction, volume registration, etc are all done
> in the volume.  The data are then mapped onto the cortical surface and
> alignment across subjects in CIFTI space for cortical data is based on
> surface registration.  Surface and volume registration are independent
> things (you are right that the surface alignment occurs using spheres),
> and the volume registration does not contribute to the cross-subject
> surface alignment.  Volume registrations can be applied to surface mesh
> coordinates exactly, so the volume to surface mapping can occur in MNI
> space (though using individual subject surfaces and individual subject
> timeseries―a very different thing than group average data to group average
> surfaces).
>
> Peace,
>
> Matt.
>
> On 4/24/15, 11:48 AM, "J.A. Etzel" <jet...@artsci.wustl.edu> wrote:
>
>> Sorry, but now I'm confused: I thought you confirmed that the HCP task
>> fMRI pipelines perform motion correction and spatial normalization (MNI
>> atlas registration) on the task fMRI images in volume space, before
>> mapping the data to the surface. Doesn't that mean that the surface
>> version of the task fMRI data relies upon the volumetric atlas
>> registration, and is so a different procedure than the spherical
>> registration to atlas space described in Anticevic et al., 2008?
>>
>> thanks,
>> Jo
>>
>>
>> On 4/24/2015 11:24 AM, Glasser, Matthew wrote:
>>> There were a few threads on this in the past.  The volume and surface
>>> registration are pretty much independent.  The cortical data are aligned
>>> with surface registration.
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: Timothy Coalson <tsc...@mst.edu <mailto:tsc...@mst.edu>>
>>> Date: Friday, April 24, 2015 at 10:55 AM
>>> To: "J.A. Etzel" <jet...@artsci.wustl.edu
>>> <mailto:jet...@artsci.wustl.edu>>
>>> Cc: Matt Glasser <glass...@wusm.wustl.edu
>>> <mailto:glass...@wusm.wustl.edu>>, "hcp-users@humanconnectome.org
>>> <mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org
>>> <mailto:hcp-users@humanconnectome.org>>
>>> Subject: Re: [HCP-Users] MNI atlas registration in volume space for task
>>> fMRI grayordinates datasets?
>>>
>>> You can't do surface registration before you have data on the surface to
>>> register with, which is what the volume to surface mapping does.  We do
>>> use surface registration, and we highly recommend its use to everyone,
>>> but volume registration is still an important preceding step - they are
>>> not mutually exclusive.
>>>
>>> Tim
>>>
>>>
>>> On Fri, Apr 24, 2015 at 10:48 AM, J.A. Etzel <jet...@artsci.wustl.edu
>>> <mailto:jet...@artsci.wustl.edu>> wrote:
>>>
>>>      Thanks for the quick reply.
>>>
>>>      Why was this chosen, as opposed to surface-based registration, such
>>> as
>>>      described in Anticevic et al. 2008
>>>      (doi:10.1016/j.neuroimage.2008.02.052)? Have you done comparisons
>>>      suggesting that volume-based registration is preferable?
>>>
>>>      thanks again,
>>>      Jo
>>>
>>>
>>>      On 4/24/2015 9:59 AM, Glasser, Matthew wrote:
>>>      > Yes that¹s how it works.
>>>      >
>>>      > Peace,
>>>      >
>>>      > Matt.
>>>      >
>>>      > On 4/24/15, 9:56 AM, "J.A. Etzel" <jet...@artsci.wustl.edu
>>> <mailto:jet...@artsci.wustl.edu>> wrote:
>>>      >
>>>      >> I have a question about the preprocessing for the task-fMRI
>>>      >> grayordinates datasets, specifically the images from the Level 2
>>>      >> fixed-effects analysis. For clarity, the images I'm asking about
>>> are
>>>      >> those like
>>>      >>
>>> /104820/MNINonLinear/Results/tfMRI_WM/tfMRI_WM_hp200_s4_level2.feat/Grayo
>>> r
>>>      >> dinatesStats/cope2.feat/pe1.dtseries.nii
>>>      >>
>>>      >>  From Barch et al. (2013) and the HCP_S500 Reference Manual,
>>> these
>>>      >> participant-level analyses were performed with a
>>> grayordinates-adapted
>>>      >> version of the FSL Level 1 and Level 2 analysis routines, using
>>> as input
>>>      >> the output of the fMRISurface pipeline.
>>>      >>
>>>      >> Which brings me to the question: Is it correct that the pipelines
>>>      >> producing these images perform (amongst other preprocessing
>>> steps)
>>>      >> motion correction and spatial normalization (MNI atlas
>>> registration) on
>>>      >> the fMRI images in volume space, before the surface mapping?
>>> Figures 19
>>>      >> and 20 in Glasser et al. (2013) suggest that this is the case,
>>> but it is
>>>      >> a bit unclear.
>>>      >>
>>>      >> thanks,
>>>      >> Jo
>>>      >>
>>>      >>
>>>      >> --
>>>      >> Joset A. Etzel, Ph.D.
>>>      >> Research Analyst
>>>      >> Cognitive Control & Psychopathology Lab
>>>      >> Washington University in St. Louis
>>>      >>http://mvpa.blogspot.com/
>>>      >> _______________________________________________
>>>      >> HCP-Users mailing list
>>>      >>HCP-Users@humanconnectome.org
>>> <mailto:HCP-Users@humanconnectome.org>
>>>      >>http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>> _______________________________________________
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

-- 
Joset A. Etzel, Ph.D.
Research Analyst
Cognitive Control & Psychopathology Lab
Washington University in St. Louis
http://mvpa.blogspot.com/
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