That is what mri_synthsr does (which is part of the FS distribution)
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Glasser, Matt
Sent: Friday, March 31, 2023 7:48 AM
To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Is it possible to add additional T1 scans to improve
surfaces/segmentation
External Email - Use Caution
I think there are some deep learning approaches out there that try to infer a
high-resolution volume from low resolution volumes in multiple planes. I don’t
know if they would work with only axial and sagittal images though.
Matt.
From:
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Michael Mc Laughlin
<mich...@thecurate.com<mailto:mich...@thecurate.com>>
Reply-To: Freesurfer support list
<Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, March 31, 2023 at 6:36 AM
To: Freesurfer support list
<Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Is it possible to add additional T1 scans to improve
surfaces/segmentation
External Email - Use Caution
I am working with standard neuro radiological MRI scans.
These typically have something like this::
a) T1 headscout volume: 1.6mmx1.6mmx1.625mm 160x160x128
b) T1 se tra 0.72x0.72x5.2 320x320x30
c) T2 tse tra scan 0.72x0.72x5.2 320x320x30
d) T2 FLAIR (dark fluid) scan 0.58x0.58x5.2 460x460x30
c) T1 tse sag 0.72x0.72x5.2 320x320x30
c) T2 tse sag 0.72x0.72x5.2 320x320x30
I have found that the best results are obtained if I do the following:
i) Start with the T1 headscout volume: 1.6mmx1.6mmx1.625mm
This produces poor pial results but much better than using the T1s with a small
number of slices.
ii) Add in the flair data: Use -FLAIR and -autorecon3 with a FLAIR MRI scan
This dramatically improves the pial surfaces and they look almost normal
iii) Add some T2 data.
This give more improvement of the pial surfaces
See attached image for how the cortex looks after these stages
My questions are:
1) How can I add in the data from the higher resolution T1 scans? (with only 30
slices)
2) If I add a second T2 scan with -T2 -T2pial -autorecon3 will the results
improve even more?
Regards,
Michael
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