On 12/5/2024 10:14 PM, JM wrote:
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Hi FreeSurfer experts,
In our hospital research settings, we collected structural MRI data
from patients while they were admitted for treatment. Some of the
patients were scanned before contrast agent was injected and some were
scanned after contrast agent was injected. There was no consistent
protocol used. Some patients had 3D T1 data collected (with dimensions
512 x 512 x 248 with voxel size 0.47 x 0.47 x 0.7), some had Ax-T1
data (with dimensions 512 x 512 x 32 with voxel size 0.4 x 0.4 x 5)
and some had only Sag-T1 data collected (with dimensions 256 x 256 x
25 with voxel size 0.85 x 0.85 x 6).
You should definitely use recon-all_clinical.sh -- this is what it is
made for. Works on any contrast too.
Interestingly, recon-all works fine without any error across all three
sets (i.e., 3D T1, Ax-T1 and Sag-T1). I would greatly appreciate
your thoughts/suggestions/answers with the following:
1. Does it matter whether images are analyzed (i.e., recon-all 'd) on
pre-contrast images or post-contrast images (in terms of output
morphometry values [e.g., thickness, volume])? In other words, would
it be OK if estimated pre-contrast morphometry values and estimated
post-contrast morphometry values can further be analyzed in group
level analysis OR subjects with pre-contrast can't be in the same
group as subjects with post-contrast for further analysis (e.g.,
morphometry vs behavior values)?
It will matter for sure, but I don't know how much. If you have two
groups, you should try to balance the groups so that each has the same
ratio of pre and post contrast. You can also test whether your behvioral
measures differ between the pre and post groups.
2. Similarly, would it be OK if estimated 3D-T1 morphometry values and
estimated Ax-T1 and Sag-T1 morphometry values can further be analyzed
in group level analysis? Otherway, I was thinking was to resample the
images to isotropic voxel size, then run recon all, and then combine
subjects with 3D-T1, Ax-T1 and Sag-T1. OR subjects with 3D-T1 can't be
in the same group as subjects with Ax-T1 and Sag-T1 for further
analysis (e.g., morphometry vs behavior values)?
Same issue as above. resampling will not solve the problem (and is what
recon-all is doing anyway).
In addition, any other suggestions on how I can utilize Ax-T1 and
Sag-T1 data for morphometry analysis would be very helpful.
I would greatly appreciate your response at your earliest convenience.
Thanks!
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