sorry for the delay, see below
On 4/14/18 10:00 AM, Boggess, Matthew Jozsef wrote:
Hello,
I just wanted to follow up to see if anyone could help with any of my
questions, particularly # 1.
Thank you!
Matt Boggess
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Boggess, Matthew
Jozsef <mbogg...@mgh.harvard.edu>
*Sent:* Thursday, April 5, 2018 8:02:07 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] fmriprep to fsfast interface
Hello,
I've been working on taking the outputs of the fmriprep
BOLD preprocessing tool
(https://fmriprep.readthedocs.io/en/latest/index.html) and coercing
them into the fsfast structure so that first levels can be run with
mkanalysis-sess and selxavg3b-sess. It's been a bit trickier than
anticipated and I was hoping to get some help verifying my current
approach (attached to this email).
Question 1:
fmriprep outputs the preprocessed BOLD data in the T1 space (mni305 is
not an option). However, the typical spatial normalization workflow
uses a registration matrix from the bold to T1 to transform to
talairach. Is there a way to do this transformation without having to
specify a registration matrix given the functional data is already in
the T1 space? My current approach is to use mri_convert with the
--apply_transform flag pointing to the talairach.xfm registration
matrix in the subject's recon folder, but I am not sure if this is a
reasonable workaround.
Do you want to analyze it in the native T1 space or in talairach space?
If native, then when you run mkanalysis-sess you can bypass the
preprocessing by directly specifying the stem of the functional data you
want to process (-funcstem). If tal space, then I think it should work
out of the box (it would recalc the registration, but that should be ok).
Question 2:
fsfast normally calculates the global mean value of the raw data to be
used for intensity normalization. However, with fmriprep I only have
access to the preprocessed data in T1 space. Would extracting the
global mean value for intensity normalization from the preprocessed
BOLD in T1 space be valid?
Yes
Question 3:
Is there a way to do first levels in the native subcortical space? If
so, what is the filename structure expected (maybe mni305.2mm gets
replaced with the subject name as with the surface data)? I've only
seen examples transforming to mni305 space, but ideally an option
would be to just transfer the preprocessed BOLD in T1 space and run
first levels staying in the native T1 space.
See above.
Thanks for your help!
Matt
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
