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Dear FreeSurfer Support Team,
Season's Greetings! I hope this email finds you well.
May I take this opportunity to seek your support regarding the use of
FreeSurfer for structural MRI data acquired using clinical epilepsy imaging
protocols with non-isotropic voxel sizes in our hospital setting.
To date, I have processed MRI data from over 90 epilepsy patients
using *FreeSurfer
v 6.0* (3T scanner 64-channel head coil, TA: 3:49 min; Voxel Size: 1.0 ×
1.0 × 0.5 mm³; Acceleration factor: 2; Relative SNR: 1.00). The
complete recon-all pipeline ran successfully for all subjects, generating
cortical and subcortical segmentations as well as quantitative statistics
files without any processing errors.
However, I learnt that 1 mm³ isotropic resolution is recommended for
optimal performance, although voxel sizes up to *1.3 × 1 × 1.3 mm³* are
considered acceptable to reduce scan time or improve signal-to-noise ratio,
as per FreeSurfer Wiki. Therefore recently, I have acquired one additional
patient data using an isotropic protocol (1.0 × 1.0 × 1.0 mm³) and compared
to epilepsy protocol mentioned above.
To conclude , I got two different quantitative values. For example, in Left
Hippocampus - Anisotropic : 3640.2 mm³ vs Isotropic : 3876.2 mm³ , Total
intracranial volume- Anisotropic : 1504943.411530 mm³ vs Isotropic :
1529703.225834 mm3 , Mean cortical thickness – Anisotropic : 2.18512 mm vs
Isotropic: 2.28844 mm.
In this context, I would greatly appreciate your guidance on the following:
1. Would you recommend resampling 1 × 1 × 0.5 mm³ images to 1 mm³
isotropic resolution prior to running recon-all, or is it fine to process
the native anisotropic resolution data?
2. Are there any appropriate FreeSurfer steps or commands to convert
my already acquired 1 × 1 × 0.5 mm³ MRI data to isotropic resolution before
running the FreeSurfer recon-all pipeline?
3. Are there any known limitations, biases, or segmentation
inaccuracies, particularly affecting hippocampal volumetry or cortical
thickness estimates, when FreeSurfer is applied to anisotropic voxel data
in epilepsy research like I did?
I am attaching the recon-all log files of both the protocols here.
Thank you very much for your time and guidance. I would greatly appreciate
your recommendations.
-- Warm regards,
*Uttara Bakshi*
*Doctoral Fellow*
*Institute Of Neurosciences Kolkata, India.*
