what was the command line and screen output of the binarization? And are you saying that pre-binarization you have locations that are above threshold, but they are set to 0 anyway?

On Thu, 28 Jan 2016, Erik Lindberg wrote:

Dear Bruce and Freesufers,

I get the following message:

surfer: Interpreting overlay volume/media/EHD/ALLA_FREESUFER_PROCESSING_TIDIS_NOMAS_AD/qdec/lh.kvot_gender.glm dir/Gend/thresholded.mgh as encoded scalar volume.

the two volumes I tried to convert:

Volume information for sig.mgh           type: MGH     dimensions: 163842 x 1 x 1    voxel sizes: 1.0000, 1.0000, 1.0000           type: FLOAT (3)            fov: 163842.000            dof: 0         xstart: -81921.0, xend: 81921.0         ystart: -0.5, yend: 0.5         zstart: -0.5, zend: 0.5             TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees        nframes: 1        PhEncDir: UNKNOWN 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

talairach xfm :  Orientation   : LIA Primary Slice Direction: coronal

voxel to ras transform:                -1.0000   0.0000   0.0000 81921.0000                 0.0000   0.0000   1.0000    -0.5000                 0.0000  -1.0000   0.0000     0.5000                 0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -1

ras to voxel transform:                -1.0000   0.0000   0.0000 81921.0000                -0.0000  -0.0000  -1.0000     0.5000                -0.0000   1.0000  -0.0000     0.5000                 0.0000   0.0000   0.0000     1.0000

Volume information for cache.th13.abs.sig.cluster.mgh           type: MGH     dimensions: 163842 x 1 x 1    voxel sizes: 1.0000, 1.0000, 1.0000           type: FLOAT (3)            fov: 163842.000            dof: 0         xstart: -81921.0, xend: 81921.0         ystart: -0.5, yend: 0.5         zstart: -0.5, zend: 0.5             TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees        nframes: 1        PhEncDir: UNKNOWN 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

talairach xfm :  Orientation   : LIA Primary Slice Direction: coronal

voxel to ras transform:                -1.0000   0.0000   0.0000 81921.0000                 0.0000   0.0000   1.0000    -0.5000                 0.0000  -1.0000   0.0000     0.5000                 0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -1

ras to voxel transform:                -1.0000   0.0000   0.0000 81921.0000                -0.0000  -0.0000  -1.0000     0.5000                -0.0000   1.0000  -0.0000     0.5000                 0.0000   0.0000   0.0000     1.0000

Although both these overlays have significant areas - nothing appears on the binarized version after the conversion

Best wishes,

Olof Lindberg

Olof Lindberg PhD Novum plan 5 NVS department section clinical geriatrics 14186 Stockholm +46722255711 MailScanner has detected a possible fraud attempt from "email.ki.se" claiming to be http://www.oloflindberg.se