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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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsmData 


Then I use subject “fsm08un”. 

I run presurfer as in MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://github.com/srikash/presurfer

Then I run 

recon-all -all -i MPRAGEised_stripped.nii.gz -s fsm08un_MPRAGEised -openmp 8





.

.

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****************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://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



If you need the recon-all.log I can send it. 

Best, 
Rene Andrade.