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