OK, I'm still at a loss. The one suspicious thing is that it only took a few min to run. So you have never looked at that volume? What is in the atlas?

On 12/16/2019 3:42 PM, Boris Rauchmann wrote:

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This is the log when I´m creating this file:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz $SUBJECTS_DIR/1122/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz
sysname  Darwin
hostname MacBook.local
machine  x86_64

setenv SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
cd /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer
mri_ca_label /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz /Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z /Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca /Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz 


== Number of threads available to mri_ca_label for OpenMP = 1 == 
reading 1 input volumes
reading classifier array from /Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca
reading input volume from /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz
reading transform from /Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 4.97
Atlas used for the 3D morph was /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca
average std = 10.8   using min determinant for regularization = 11.7
0 singular and 129 ill-conditioned covariance matrices regularized
labeling volume...
0 gm and wm labels changed (%nan to gray, %nan to white out of all changed labels)
0 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 9576 changed.
pass 2: 3286 changed.
MRItoUCHAR: min=0, max=246
MRItoUCHAR: converting to UCHAR
writing labeled volume to /Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz
mri_ca_label utimesec    146.184667
mri_ca_label stimesec    1.040963
mri_ca_label ru_maxrss   1436573696
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   609288
mri_ca_label ru_majflt   112
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  0
mri_ca_label ru_oublock  4
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    3
mri_ca_label ru_nivcsw   36417
auto-labeling took 2 minutes and 28 seconds.

This is what I get when I do mrs_info on the gas:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_info /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gca 
reading frame -1 of gca
Volume information for /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gca
          type: GCA
    dimensions: 256 x 256 x 256 x 3
   voxel sizes: 1.000000, 1.000000, 1.000000
          type: FLOAT (3)
           fov: 256.000
           dof: 0
        xstart: -128.0, xend: 128.0
        ystart: -128.0, yend: 128.0
        zstart: -128.0, zend: 128.0
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
       nframes: 3
       PhEncDir: UNKNOWN
       FieldStrength: 0.000000
ras xform present
    xform info: x_r =  -1.0000, y_r =   0.0000, z_r =   0.0000, c_r =     0.0000
              : x_a =   0.0000, y_a =   0.0000, z_a =   1.0000, c_a =     0.0000
              : x_s =   0.0000, y_s =  -1.0000, z_s =   0.0000, c_s =     0.0000
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
               -1.0000   0.0000   0.0000   128.0000
                0.0000   0.0000   1.0000  -128.0000
                0.0000  -1.0000   0.0000   128.0000
                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -1

ras to voxel transform:
               -1.0000  -0.0000  -0.0000   128.0000
               -0.0000  -0.0000  -1.0000   128.0000
               -0.0000   1.0000  -0.0000   128.0000
               -0.0000  -0.0000  -0.0000     1.0000




Am 16.12.2019 um 21:21 schrieb Boris Rauchmann <boris.rauchmann@gmail.com>:

Thanks, it was created using: 

mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz

Best,
Boris


Am 16.12.2019 um 21:12 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>:

There is something weird about that file. How was it created?
doug
ps. Please include previous correspondence in the email

On 12/16/19 1:12 PM, Boris Rauchmann wrote:

        External Email - Use Caution

Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz
mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz,
-1): could not open file

Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D.
<DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>:

mri_info N_Atlas_subcotex.mgz


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