cd /usr/local/freesurfer/subjects


 mri_convert im00001.dcm sample-001.nii.gz



 recon-all -i sample-001.nii.gz -s bert -all


  recon-all -s bert -hippocampal-subfields-T1 

  recon-all -s bert -brainstem-structures 

  recon-all -s bert -hippocampal-subfields-T1 -brainstem-structures 


   2.18288e-11 3.00003 2.2352e-08 
  Offset: [125.764, -50.0129, -86.838]
  Center: [0, 0, 0]
  Translation: [125.764, -50.0129, -86.838]
  Inverse: 
    -0.33333 -7.10858e-26 -9.70118e-11 
    2.42528e-12 2.4835e-09 0.33333 
    -2.06795e-25 -0.33333 2.4835e-09 
  Singular: 0
I am WriteImage and I'm running! 
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
This file does not contain MRI parameters
numberOfLabels: 25
Rasterizing mesh...here: 25
here2: 25
done
mri_convert.bin discreteLabels.mgz discreteLabelsResampledT1.mgz -rt nearest -odt float -rl /usr/local/freesurfer/subjects/kapranoupanagiota_vol/mri/norm.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from discreteLabels.mgz...
TR=6.64, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 7.27596e-12, 9.69362e-27)
j_ras = (-7.75489e-26, 7.45058e-09, -1)
k_ras = (-2.91038e-10, 1, 7.45058e-09)
reading template info from volume /usr/local/freesurfer/subjects/kapranoupanagiota_vol/mri/norm.mgz...
Reslicing using nearest 
writing to discreteLabelsResampledT1.mgz...
mv: cannot stat 'volumesAmygdala.txt': No such file or directory
Everything done!
It took 649.3659 seconds 

Started at Fri Sep 14 02:00:57 EDT 2018 
Ended   at Fri Sep 14 02:32:48 EDT 2018
#@#%# recon-all-run-time-hours 0.531
recon-all -s kapranoupanagiota_vol finished without error at Fri Sep 14 02:32:48 EDT 2018
done
brain@neurodebian:~$ 1