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