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:
External Email - Use Caution
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.rauchm...@gmail.com<mailto:boris.rauchm...@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
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz
Best,
Boris
Am 16.12.2019 um 21:12 schrieb Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>:
There is something weird about that file. How was it created?
doug
ps. Please include previous correspondence in the email
On 12/16/19 1:12 PM, Boris Rauchmann wrote:
External Email - Use Caution
Boriss-MacBook-Pro:mri boris$ 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.
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>>:
mri_info N_Atlas_subcotex.mgz
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