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Hello FreeSurfer Developers,
I am attempting to perform longitudinal analysis of brain volumes with two timepoints for each patient. Some of these patients were scanned using different scanners. When creating a base file for longitudinal analysis, I encounter the following error:
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 rca-base-init 7.4.1 Darwin Kayas-MacBook-Pro.local 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:32:11 PDT 2023; root:xnu-10002.41.9~7/RELEASE_ARM64_T6030 arm64 pid 3979 #-------------------------------------------- #@# Longitudinal Base Subject Creation Sat Jul 6 15:59:22 +03 2024 /Users/kayaacademia/Desktop/MS_LAB/10402969_base \n mri_diff --notallow-pix --notallow-geo /Users/kayaacademia/Desktop/MS_LAB/10402969_22/mri/rawavg.mgz /Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/rawavg.mgz \n error: mghRead(/Users/kayaacademia/Desktop/MS_LAB/10402969_22/mri/rawavg.mgz, -1): could not open file \n******************************************************************************* WARNING: Image parameters differ across time, maybe due to acquisition changes? Consistent changes in, e.g., resolution can potentially bias a longitudinal study! You can check image parameters by running mri_info on each input image. Will continue in 10 seconds ... *******************************************************************************\n \n mri_robust_template --mov /Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz /Users/kayaacademia/Desktop/MS_LAB/10402969_22/mri/norm.mgz --lta /Users/kayaacademia/Desktop/MS_LAB/10402969_base/mri/transforms/10402969_19_to_10402969_base.lta /Users/kayaacademia/Desktop/MS_LAB/10402969_base/mri/transforms/10402969_22_to_10402969_base.lta --template /Users/kayaacademia/Desktop/MS_LAB/10402969_base/mri/norm_template.mgz --average 1 --sat 4.685 \n 7.4.1
--mov: Using /Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz as movable/source volume. --mov: Using /Users/kayaacademia/Desktop/MS_LAB/10402969_22/mri/norm.mgz as movable/source volume. Total: 2 input volumes --lta: Will output LTA transforms --template: Using /Users/kayaacademia/Desktop/MS_LAB/10402969_base/mri/norm_template.mgz as template output volume. --average: Using method 1 for template computation. --sat: Using saturation 4.685 in M-estimator! reading source '/Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz'... error: mghRead(/Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz, -1): could not open file error: MultiRegistration::loadMovables: could not open input volume /Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz.
ERROR: Darwin Kayas-MacBook-Pro.local 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:32:11 PDT 2023; root:xnu-10002.41.9~7/RELEASE_ARM64_T6030 arm64
recon-all -s 10402969_base exited with ERRORS at Sat Jul 6 15:59:33 +03 2024
I have attached the recon-all.log file for your reference. I am not a data scientist and am unable to determine the cause of this issue. I would greatly appreciate your guidance on how to resolve this error.
1. *FreeSurfer version:* freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 2. *Platform:* macOS 23.1.0 3. *uname -a:* Darwin Kayas-MacBook-Pro.local 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:32:11 PDT 2023; root .41.9~7/RELEASE_ARM64_T6030 arm64 4. *recon-all.log:* see attached
Thank you for your assistance, much appreciated.
Best regards,
Ahmet Kaya, MD