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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).
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)?
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)?
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!
On 12/5/2024 10:14 PM, JM wrote:
External Email - Use Caution
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:
- 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.
- 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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Douglas N. Greve -
JM