External Email - Use Caution
Thank you for your response. I already followed the path in the link provided in your email. All time points are already processed with recon-all. What I could see is the error is regarding that the norm.mgz can not be read, however I can open it with freeview.
I would appreciate your guidance on this matter.
Best, Ahmet
On Mon, 8 Jul 2024 at 2:38 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
It looks like you are trying to create the base for two timepoints - ‘/Applications/freesurfer/7.4.1/bin/recon-all -base 10402969_base -tp 10402969_19 -tp 10402969_22 -all’.
I’m assuming each timepoint has been cross-sectionally processed - https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing
Best,
Yujing
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Ahmet Kaya *Sent:* Sunday, July 7, 2024 9:23 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Longitudinal Analysis Error
External Email - Use Caution *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.
- *FreeSurfer version:*
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
- *Platform:* macOS 23.1.0
- *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
- *recon-all.log:* see attached
Thank you for your assistance, much appreciated.
Best regards,
Ahmet Kaya, MD
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