Hi all,
I wonder if people have any data (or anecdotes - I'm not picky) with regard to how high of resolution T2w or FLAIR images need to be in order to be useful for FreeSurfer's pial refinement. I've seen a couple threads suggesting the optimal is ~1mm isotropic, and that thick slice (1x1x5 mm^3) FLAIR images could be tried, but might hurt more than help, and I'm wondering if there's a suboptimal-but-still-useful range somewhere in between.
For the record, this isn't a question of what scan parameters are recommended, but rather is in the context of data that's already been collected, which I would like to preprocess as well as possible.
So, at what resolutions would you recommend (a) completely ignoring T2w/FLAIR images; (b) including T2w/FLAIR images that pass QC; (c) trying and seeing? Do these answers change at all with T1w resolution?
-- Chris Markiewicz Center for Reproducible Neuroscience Stanford University
The trouble with highly anisotropic resolutions is that your resolution is only as good as your worst axis for the convoluted cerebral cortex. 0.8mm or better would be optimal given a minimum cortical thickness of 1.6mm.
You can always try with what you have and see if it is net beneficial or not.
Peace,
Matt.
On 2/28/18, 12:40 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Christopher Markiewicz" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of markiewicz@stanford.edu> wrote:
Hi all,
I wonder if people have any data (or anecdotes - I'm not picky) with regard to how high of resolution T2w or FLAIR images need to be in order to be useful for FreeSurfer's pial refinement. I've seen a couple threads suggesting the optimal is ~1mm isotropic, and that thick slice (1x1x5 mm^3) FLAIR images could be tried, but might hurt more than help, and I'm wondering if there's a suboptimal-but-still-useful range somewhere in between.
For the record, this isn't a question of what scan parameters are recommended, but rather is in the context of data that's already been collected, which I would like to preprocess as well as possible.
So, at what resolutions would you recommend (a) completely ignoring T2w/FLAIR images; (b) including T2w/FLAIR images that pass QC; (c) trying and seeing? Do these answers change at all with T1w resolution?
-- Chris Markiewicz Center for Reproducible Neuroscience Stanford University
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I would add that my guess is the FLAIR is helpful up to about 1.25-1.5mm thickest dimension
cheers Bruce
On Wed, 28 Feb 2018, Glasser, Matthew wrote:
The trouble with highly anisotropic resolutions is that your resolution is only as good as your worst axis for the convoluted cerebral cortex. 0.8mm or better would be optimal given a minimum cortical thickness of 1.6mm.
You can always try with what you have and see if it is net beneficial or not.
Peace,
Matt.
On 2/28/18, 12:40 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Christopher Markiewicz" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of markiewicz@stanford.edu> wrote:
Hi all,
I wonder if people have any data (or anecdotes - I'm not picky) with regard to how high of resolution T2w or FLAIR images need to be in order to be useful for FreeSurfer's pial refinement. I've seen a couple threads suggesting the optimal is ~1mm isotropic, and that thick slice (1x1x5 mm^3) FLAIR images could be tried, but might hurt more than help, and I'm wondering if there's a suboptimal-but-still-useful range somewhere in between.
For the record, this isn't a question of what scan parameters are recommended, but rather is in the context of data that's already been collected, which I would like to preprocess as well as possible.
So, at what resolutions would you recommend (a) completely ignoring T2w/FLAIR images; (b) including T2w/FLAIR images that pass QC; (c) trying and seeing? Do these answers change at all with T1w resolution?
-- Chris Markiewicz Center for Reproducible Neuroscience Stanford University
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Christopher Markiewicz -
Glasser, Matthew