==============================
==> mri2mesh started  Tue Jul 26 10:35:56 UTC 2022 ...
==============================
command line options: --all ernie /mnt/imagedata/simnibs_examples/ernie/org/ernie_T2.nii.gz
 
==============================
==> --brain/--brainf: Preparing GM and WM surfaces ...
==============================
 
==============================
==> running FreeSurfer recon-all on T1fs! ...
==============================

fslmaths /mnt/imagedata/simnibs_examples/ernie/org/ernie_T2.nii.gz /home/gianrocco/m2m_ernie/T1fs

fslreorient2std /home/gianrocco/m2m_ernie/T1fs /home/gianrocco/m2m_ernie/T1fs

fslswapdim /home/gianrocco/m2m_ernie/T1fs x -z y /home/gianrocco/m2m_ernie/tmpImg

mri_convert -cs 1 /home/gianrocco/m2m_ernie/tmpImg.nii.gz /home/gianrocco/m2m_ernie/tmpImg.nii.gz

mri_convert -cm /home/gianrocco/m2m_ernie/tmpImg.nii.gz /home/gianrocco/m2m_ernie/tmpImg.nii.gz

rm /home/gianrocco/m2m_ernie/tmpImg.nii.gz

fslswapdim /home/gianrocco/m2m_ernie/T1fs x -z y /home/gianrocco/m2m_ernie/tmpImg

mri_convert -nc -cs 1 -oni 256 -onj 256 -onk 256 -rt cubic /home/gianrocco/m2m_ernie/tmpImg.nii.gz /home/gianrocco/m2m_ernie/T1fs_resamp.nii.gz

fslswapdim /home/gianrocco/m2m_ernie/T1fs_resamp x z -y /home/gianrocco/m2m_ernie/T1fs_resamp

rm /home/gianrocco/m2m_ernie/tmpImg.nii.gz

fslorient -setqform -1 0 0 128.000000 0 1 0 -128.000000 0 0 1 -127.000000 0 0 0 1 /home/gianrocco/m2m_ernie/T1fs_resamp

fslorient -setsform -1 0 0 128.000000 0 1 0 -128.000000 0 0 1 -127.000000 0 0 0 1 /home/gianrocco/m2m_ernie/T1fs_resamp

flirt -in /usr/local/fsl/data/standard/MNI152_T1_1mm.nii.gz -ref /home/gianrocco/m2m_ernie/T1fs_resamp -out /home/gianrocco/m2m_ernie/tmp/MNIfs_reg
error code 137
exiting mri2mesh

 
==============================
==> mri2mesh started  Tue Jul 26 10:37:25 UTC 2022 ...
==============================
command line options: --all ernie /mnt/imagedata/simnibs_examples/ernie/org/ernie_T2.nii.gz
 
==============================
==> --brain/--brainf: Preparing GM and WM surfaces ...
==============================
 
==============================
==> running FreeSurfer recon-all on T1fs! ...
==============================

fslmaths /mnt/imagedata/simnibs_examples/ernie/org/ernie_T2.nii.gz /home/gianrocco/m2m_ernie/T1fs

fslreorient2std /home/gianrocco/m2m_ernie/T1fs /home/gianrocco/m2m_ernie/T1fs

fslswapdim /home/gianrocco/m2m_ernie/T1fs x -z y /home/gianrocco/m2m_ernie/tmpImg

mri_convert -cs 1 /home/gianrocco/m2m_ernie/tmpImg.nii.gz /home/gianrocco/m2m_ernie/tmpImg.nii.gz

mri_convert -cm /home/gianrocco/m2m_ernie/tmpImg.nii.gz /home/gianrocco/m2m_ernie/tmpImg.nii.gz

rm /home/gianrocco/m2m_ernie/tmpImg.nii.gz

fslswapdim /home/gianrocco/m2m_ernie/T1fs x -z y /home/gianrocco/m2m_ernie/tmpImg

mri_convert -nc -cs 1 -oni 256 -onj 256 -onk 256 -rt cubic /home/gianrocco/m2m_ernie/tmpImg.nii.gz /home/gianrocco/m2m_ernie/T1fs_resamp.nii.gz

fslswapdim /home/gianrocco/m2m_ernie/T1fs_resamp x z -y /home/gianrocco/m2m_ernie/T1fs_resamp

rm /home/gianrocco/m2m_ernie/tmpImg.nii.gz

fslorient -setqform -1 0 0 128.000000 0 1 0 -128.000000 0 0 1 -127.000000 0 0 0 1 /home/gianrocco/m2m_ernie/T1fs_resamp

fslorient -setsform -1 0 0 128.000000 0 1 0 -128.000000 0 0 1 -127.000000 0 0 0 1 /home/gianrocco/m2m_ernie/T1fs_resamp

flirt -in /usr/local/fsl/data/standard/MNI152_T1_1mm.nii.gz -ref /home/gianrocco/m2m_ernie/T1fs_resamp -out /home/gianrocco/m2m_ernie/tmp/MNIfs_reg

fslroi /home/gianrocco/m2m_ernie/T1fs_resamp /home/gianrocco/m2m_ernie/T1fs_roi 0 -1 0 -1 72 184

fslcreatehd 256 256 72 1 1 1 1 1 0 0 0 16 /home/gianrocco/m2m_ernie/tmpImg

fslmerge -z /home/gianrocco/m2m_ernie/T1fs_roi /home/gianrocco/m2m_ernie/tmpImg /home/gianrocco/m2m_ernie/T1fs_roi

rm /home/gianrocco/m2m_ernie/tmpImg.nii.gz

fslcpgeom /home/gianrocco/m2m_ernie/T1fs_resamp /home/gianrocco/m2m_ernie/T1fs_roi

fslswapdim /home/gianrocco/m2m_ernie/T1fs_roi x -z y /home/gianrocco/m2m_ernie/tmp/T1fs_roi_FS

recon-all -i /home/gianrocco/m2m_ernie/tmp/T1fs_roi_FS.nii.gz -s /home/gianrocco/fs_ernie

recon-all -s /home/gianrocco/fs_ernie -all -3T -cubic -cm
error code 1
exiting mri2mesh

 
==============================
==> mri2mesh started  Tue Jul 26 12:29:28 UTC 2022 ...
==============================
command line options: -c ernie
 
==============================
==> --check: Opening freeview to check the quality of the segmentation. ...
==============================
 
==============================
==> mri2mesh started  Tue Jul 26 12:31:06 UTC 2022 ...
==============================
command line options: -c ernie
 
==============================
==> --check: Opening freeview to check the quality of the segmentation. ...
==============================