[Camino-users] sfplot warning/error

[Seunarine, Kiran]

Hi Zhuang,

Sorry for the slow reply.  With regard to your first question, what command did you use to create the FA map?  The standard command, i.e.

fa < dwi.Bfloat > fa.img

should output the FA as big-endian doubles.  If you used a different command (for example, you set -outputdatatype or piped the output through voxel2image) then the you have to adjust the data type in the subsequent commands.  I will add the DTI commands we used to the multi-fibre tutorial to avoid any further confusion.

To create different views in sfplot, you will need to use Camino's shredder utility to extract the correct information.  So, to obtain a coronal view, the commands are

# coronal image (slice 61) - read 11th row of each axial slice
sliceOffset=60
shredder $((sliceOffset*112*4)) $((1*112*4)) $((111*112*4)) < fa.img > cor_fa.Bfloat
shredder $((sliceOffset*112*(246+2)*8)) $((1*112*(246+2)*8)) $((111*112*(246+2)*8)) < dwi_ODFs.Bdouble > cor_dwi_ODFs.Bdouble

The shredder command above skips the first 60 rows, reads a row, then skips the next 111 rows.  This gives you one coronal slice.  You can select other slices by adjusting the initial offset.

# plot as usual, but remember to update -projection so that the ODFs are being viewed from the correct direction!
sfplot -inputmodel rbf -rbfpointset 246 -rbfsigma 0.2618 -xsize 50 -ysize 112 -minifigsize 30 30 -minifigseparation 2 2 -minmaxnorm -dircolcode -projection 3 -2 -backdrop cor_fa.Bfloat < cor_dwi_ODFs.Bdouble > cor_dwi_ODFs.rgb

convert -depth 8 -size 3584x1600 cor_dwi_ODFs.rgb cor_dwi_ODFs.png

The procedure is the same for the sagittal view:

# sagittal image (slice 61) - read 61st element of each axial row of data
sliceOffset=60
shredder $((sliceOffset*4)) $((1*4)) $((111*4)) < fa.img > sag_fa.Bfloat
shredder $((sliceOffset*(246+2)*8)) $((1*(246+2)*8)) $((111*(246+2)*8)) < dwi_ODFs.Bdouble > sag_dwi_ODFs.Bdouble

The shredder command for the sagittal view follows the same principle.  First, you skip a given number of voxels in a row.  You then read a single voxel and then skip another 111 voxels (in this example there are 112 voxels in a row).  As before, the command gives you the data for a single slice of the volume and the offset controls the slice.

# again, remember to update -projection so that the ODFs are being viewed from the correct direction!
sfplot -inputmodel rbf -rbfpointset 246 -rbfsigma 0.2618 -xsize 50 -ysize 112 -minifigsize 30 30 -minifigseparation 2 2 -minmaxnorm -dircolcode -projection 3 -1 -backdrop sag_fa.Bfloat < sag_dwi_ODFs.Bdouble > sag_dwi_ODFs.rgb

convert -depth 8 -size 3584x1600 sag_dwi_ODFs.rgb sag_dwi_ODFs.png

Hope that helps.

Kiran
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