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.glmdir/Gend/thresholded.mgh as encoded scalar volume.


the two volumes I tried to convert: 

1)

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


2)


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
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