Can you check if the file exists – ‘ ls -l /Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz’?

 

Can you attach the recon-all.log for both timepoints and the base processing?

 

Yujing

 

 

 

 

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ahmet Kaya
Sent: Wednesday, July 10, 2024 12:45 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Longitudinal Analysis Error

 

        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.

  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

  1. recon-all.log: see attached

Thank you for your assistance, much appreciated.

 

Best regards,

Ahmet Kaya, MD

 

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