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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ahmet Kaya Sent: Sunday, July 7, 2024 9:23 AM To: freesurfer@nmr.mgh.harvard.edumailto: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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