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Dear Freesurfer experts:
I am having trouble processing with recon-all the file I obtain with presurfer from an MP2RAGE. I don’t know if you have any experience with this. The data I obtained from this https://secure-web.cisco.com/1DoAeFvUHnYto_t5xoLbWcFtbuOwQtmlS1ENoWBmeeHffDp...
Then I use subject “fsm08un”.
I run presurfer as in https://secure-web.cisco.com/1avsRdF8F2mgWmm0OUulJTd3eZF6z9U3j9ezKhlvZi12HC0...
Then I run
recon-all -all -i MPRAGEised_stripped.nii.gz -s fsm08un_MPRAGEised -openmp 8
. . .
****************TEMPLATE DEFORMATION****************
second estimation of the COG coord: x=130,y=125, z=130, r=124102 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1447023003 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1862269955 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -230683617 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1409286624 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 943723776 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 943755195 mri_watershed Error: GLOBAL region of the brain empty ! Darwin Renes-MacBook-Air.local 22.5.0 Darwin Kernel Version 22.5.0: Thu Jun 8 22:22:19 PDT 2023; root:xnu-8796.121.3~7/RELEASE_ARM64_T8103 arm64
recon-all -s fsm08un_MPRAGEised exited with ERRORS at Tue Aug 1 15:40:57 CEST 2023
For more details, see the log file /Applications/freesurfer/7.3.2/subjects/fsm08un_MPRAGEised/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1t6IHvg5_DeUlvFUHchBUPV_vqGqDEzbhHz1e6IOApGryD_X...
If you need the recon-all.log I can send it.
Best, Rene Andrade.