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Hello,
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.iomailto:suzannewitt@flywheel.io she/her flywheel.iohttps://secure-web.cisco.com/1lauWKjXr4_chpBjaaXEv16-WgEUjyLdWrrdE7rj4CoASOaCQtS6HRJ7h2ZsSxWHY9hPNv94yzXTH_0sR2v9i3g6fCh16Khi8dTq5lfaKGNlmW9P_G0y2kv_iAgfO21c529PstqbxwBVCht18Ztz1ETbGbnXtfCytFM7BMjXgvKKjOt63p5PeLXzxqp2MYKKY7FbmcqSqpcdTqR2Tr6nzX-c50ctcEUZH2UX8GwI9P6far7n25tSU2sWcBIkg2nzq-55cW7Q8DZvOhR7ieJWxN9qRkpRTn55_okW9-Bp3LvwGbwuqU8JyC_iPDJJJ32x2/https%3A%2F%2Fflywheel.io%2F%3Futm_source%3Demail%26utm_medium%3Dsignature%26utm_campaign%3Demployeesignature [A close-up of a logo Description automatically generated] Sign up to receive our monthly updateshttps://secure-web.cisco.com/1yipTZHLgLQzEDOTwlegpN9Mp4brS1wWsbahzxQ9yRI6Gui9Avgn8jXKzKSUji2wBBvoOkGJC8lMOrTZxYrEQiAlXiEvUBkA1sDb6cGVdYrSRFhLZhlN5JpzDlPiGkomTnfGpEOHf9UFl2p4YGVS7Z5Tji5-eAwFVRHvyNR4Z_wBe351NB6ECKhs68oqt5d2ZZgb56hCyFKpkWJT2M08ihna3nLVvP0p1O_vX8UKFQEMNhRqlSBL0Oq6zrP-xcTevdzdMjIjyvmYwZF8DXn0Tl7vgIZ-98iijyykc0hOxDZPuozIw62HQLJS-OFvXFEZZ/https%3A%2F%2Fflywheel.io%2Fsubscribe-to-newsletter%2F%3Futm_source%3Demail%26utm_medium%3Dsignature%26utm_campaign%3Demployeesignature
