Dear Amir,
These are excellent questions.
The module was written with ADNI in mind, so that’s good news for you!
Question 1: Things may have gotten better since I last looked into the high-res T2s in ADNI, but back in the day, it was super-common to see fields of view that did not completely cover the hippocampus. Therefore, I would keep USE_T1=1; otherwise, the measured volumes will not consider the full hippocampus.
Question 2: yeah it means “coarsely aligned in scanner (world) coordinates”, which they definitely are in ADNI. So you don’t have to do anything. The module will handle the rigid registration for you.
Kind regards,
/Eugenio
-- Juan Eugenio Iglesias http://www.jeiglesias.com
From: AmirHussein Abdolalizadeh amirhussein.a@gmail.com Date: Wednesday, July 9, 2025 at 2:57 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] SegmentHA_T2: USE_T1 and T2 alignment in ADNI data
External Email - Use Caution Dear FreeSurfer users/experts,
I have two questions related to the manual of segmentHA_T2.sh pipeline written on the FreeSurfer's website, which I would like to apply to ADNI data. I couldn't find any solutions to that elsewhere. Regarding the data, T1s have a resolution of 1.2 x 1.05 x 1.05 and T2s have a limited FoV on Hippocampus/Amygdala with a voxel size of 0.4 x 2 x 0.4.
I have two questions:
1. What value should I set for USE_T1? According to the manual on FreeSurfer's website: "Using the main T1 is advised when the additional scan is of comparable resolution as the T1, or when the additional scan does not cover the whole hippocampal region - in that case, the T1 information will be critical to segment the hippocampal regions outside the field of view of the additional volume. Using the additional scan in isolation is advised when it is of higher resolution than the T1 while covering the whole hippocampi and amygdalae."
Based on this text and ADNI's high-resolution T2, what should I set USE_T1 to? 2. Regarding the additional scan, it is written that: "In this case, the only requirement is that the additional scan is coarsely aligned to the main T1 scan." What does it mean by "coarsely aligned"? Should I linearly register the T2 to T1? However, visualizing the T1 and T2 images overlaid on top of each other reveals that they are somewhat aligned, as both T1 and T2 were acquired in the same session; however, they are not as aligned as one would expect after a rigid transformation.
Looking forward to your comments.
Best, Amir