On Tue, Dec 17, 2019 at 6:33 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

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:

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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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