Can you send me the subject data following these steps?
From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.
On 12/20/2019 10:58 AM, Boris Rauchmann wrote:
External Email - Use Caution
I had a look at the mgz file with freeview and it actually looks fine to me.
Its the subcortical segmentation of the BN atlas.
Do you have any ideas what went wrong?
Best,
Boris
On Tue, Dec 17, 2019 at 6:33 PM Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> wrote:
OK, I'm still at a loss. The one suspicious thing is that it only took a few
min to run. So you have never looked at that volume? What is in the atlas?
On 12/16/2019 3:42 PM, Boris Rauchmann wrote:
External Email - Use Caution
This is the log when I´m creating this file:
Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ 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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