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Dear FreeSurfer Developers,
I am trying to run the recon-all pipeline on some MP2RAGE images, which have been regularised using the robust reconstruction, in order to avoid the salt and pepper noise in the background.
I am running the beta-version of FS 8, and have followed the instructions, including "export FS_ALLOW_DEEP=1”. Synthstrip runs extremely slow, but finishes. I also get a lot of other mgz images :
ls /Volumes/SanDiskSSD1/Freesurfer/subjetcs/sub-0271/mri T1.mgz mri_nu_correct.mni.log orig rawavg.mgz synthseg.rca.mgz tmp.mri_mcadura_seg.50836 aseg.auto_noCCseg.mgz nu.mgz orig.mgz rawavg2orig.lta synthstrip.mgz transforms
But after a while the job crashes with the message:
Node: 'unet/unet_bn_down_0/FusedBatchNormV3' 2 root error(s) found. (0) INVALID_ARGUMENT: input must be 4-dimensional[1,72,72,72,24] [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]] [[unet/unet_conv_downarm_2_1/BiasAdd/_44]] (1) INVALID_ARGUMENT: input must be 4-dimensional[1,72,72,72,24] [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]] 0 successful operations. 0 derived errors ignored. [Op:__inference_predict_function_1146]
Installation details: 1) FreeSurfer version: MacOS X darwin arm64 (64b) PKG installer 2) Platform:macOS Séquoia version Version 15.1.1 32GB RAM 3) uname -a: Darwin iMac-Fam-Lund.local 24.1.0 Darwin Kernel Version 24.1.0: Thu Nov 14 18:19:02 PST 2024; root:xnu-11215.41.3~13/RELEASE_ARM64_T8132 arm64 4) recon-all.log: see attached
I am new to Freesurfer, and really hope you can help.
Best Torben Lund
Torben Ellegaard Lund Associate Professor, PhD Center of Functionally Integrative Neuroscience (CFIN) Aarhus University Aarhus University Hospital Palle Juul Jensens Boulevard 99 J117 krydspunkt J117 8200 Aarhus N Denmark