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Hi, I want to do coregistration with my eeg and icbm mri template, i dont have subject mri. My epo.fif file has eeg digmontage with 63 eeg channels and fiducilas. I wanna create trans.fif to proceed with source localization. Can anyone tell me how can i validate the result of my trans.fif. I locked the default loaded fiducial of MRI. I loaded the epo.fif file, used 3 axis scaling mode because iam using template mri, then fit icp with scaling, then under the translation and rotation fitted fiducial and icp. I attached the output.
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On Fri, Sep 5, 2025 at 11:48 PM Suzanne Witt suzannewitt@flywheel.io wrote:
External Email - Use CautionHello,
I have previously been running Freesurfer 7.4.1 Ubuntu 20 from a Docker container on a GCP n1-highmem-4 machine (4 CPUs, 26GB RAM, 207GB Disk, 32GB Swap) with no issues. I recently updated the Docker image to install Freesurfer 7.4.1 Ubuntu 22 from the official distribution, and now “recon-all” is getting stuck after mri_nu_correct.mni completes and at the very start of “mri_add_xform_to_header -c /usr/local/freesurfer/subjects/05/mri/transforms/talairach.xfm nu.mgz nu.mgz”.
Currently, in order to get Freesurfer 7.4.1 Ubuntu 22 to run to completion, I am having to launch the jobs on a GCP n1-highmem-8 machine (8 CPUs, 52GB RAM, 207GB Disk, 32GB Swap).
I am not seeing anything in either the release notes or the message boards to suggest that the Ubuntu 22 version of Freesurfer 7.4.1 has additional memory requirements compared with the Ubuntu 20 version. I have tested reducing both of the omp threads and itk threads from 4 to 2. I am also not running with the “parallel” flag. Are there any other options that can be used to reduce the memory usage of the Ubuntu 22 version of Freesurfer 7.4.1?
I’ve attached a typical log file showing the recon-all workflow getting stuck at the “mri_add_xform_to_header” step.
cheers.
Suzanne T. Witt, PhD
Scientific Solutions Engineer
suzannewitt@flywheel.io
she/her
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