So just to see if I understood your point, If I use surfaces in
${StudyFolder}/${Subject}/T1w/fsaverage_LR32k for probtrackx, then there is no
need to provide –xfm and —inxfm transform arguments? Or do I still need to run
FNIRT between diffusion space and T1w and use the results in —xfm and —xfm
arguments of probtrackx?
From: "Glasser, Matthew" <[email protected]<mailto:[email protected]>>
Date: Tuesday, November 1, 2016 at 7:41 PM
To: "Shadi, Kamal" <[email protected]<mailto:[email protected]>>,
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data
The MMP1.0 ROIs are not registered to a 3D average brain. They exist on a 2D
standard surface mesh. I mention below the individual subject versions of this
surface mesh that you could use for tractography. In that case, you would use
the white matter surface as your waypoint and the pial surface as your stop.
Peace,
Matt.
From: "Shadi, Kamal" <[email protected]<mailto:[email protected]>>
Date: Tuesday, November 1, 2016 at 6:39 PM
To: Matt Glasser <[email protected]<mailto:[email protected]>>,
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data
My plan is indeed to run probtrackx using surface ROIs. But since HCP diffusion
data is not registered to the average brain template of the MMP1.0 ROIs, my
question is what is the recommended way of running FNIRT for doing so? What is
the appropriate template file(T1w)? And is there any config file HCP releases
to be used by FNIRT?
From: "Glasser, Matthew" <[email protected]<mailto:[email protected]>>
Date: Tuesday, November 1, 2016 at 7:29 PM
To: "Shadi, Kamal" <[email protected]<mailto:[email protected]>>,
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data
You can map the parcellation from the surface to the volume using the white and
pial surfaces in ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k and the
ribbon-based option. Also, some tractography tools like probtrackx allow you
to track directly to surface ROIs (which is better).
Peace,
Matt.
From: "Shadi, Kamal" <[email protected]<mailto:[email protected]>>
Date: Tuesday, November 1, 2016 at 6:27 PM
To: Matt Glasser <[email protected]<mailto:[email protected]>>,
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data
Hi Matt.,
Yes, It is an HCP subject.
Thanks,
Kamal
From: "Glasser, Matthew" <[email protected]<mailto:[email protected]>>
Date: Tuesday, November 1, 2016 at 7:25 PM
To: "Shadi, Kamal" <[email protected]<mailto:[email protected]>>,
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data
Is this an HCP subject or another subject?
Peace,
Matt.
From:
<[email protected]<mailto:[email protected]>>
on behalf of "Shadi, Kamal"
<[email protected]<mailto:[email protected]>>
Date: Tuesday, November 1, 2016 at 12:18 AM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: [HCP-Users] FNIRT for HCP diffusion data
Hi all,
I am trying to run probtrackx using HCP preprocessed diffusion data and MMP1.0
ROIs.
To my understanding the corresponding T1w image of MMP1.0 ROIs is:
HCP_PhaseTwo / Q1-Q6_RelatedParcellation210 / MNINonLinear /
Q1-Q6_RelatedParcellation210_AverageT1w_restore.nii.gz
Is this a right choice?
Now I want to register a subject diffusion.bedpostx directory to the MMP1.0 ROI
space using FNIRT.
Is there an HCP config file for the FNIRT registration? If not any recommended
settings?
Any pointer is much appreciated.
Thanks,
Kamal Shadi
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