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<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Hi Zhuang,<br>
<br>
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.<br>
<br>
<span style="color: rgb(128, 128, 128); font-family: Courier New;">fa < dwi.Bfloat > fa.img</span><br>
<br>
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.<br>
<br>
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<br>
<br>
<span style="color: rgb(0, 128, 0); font-family: Courier New;"># coronal image (slice 61) - read 11th row of each axial slice</span><br style="color: rgb(128, 128, 128); font-family: Courier New;">
<span style="color: rgb(128, 128, 128); font-family: Courier New;">sliceOffset=60</span><br style="color: rgb(128, 128, 128); font-family: Courier New;">
<span style="color: rgb(128, 128, 128); font-family: Courier New;">shredder $((sliceOffset*112*4)) $((1*112*4)) $((111*112*4)) < fa.img > cor_fa.Bfloat</span><br style="color: rgb(128, 128, 128); font-family: Courier New;">
<span style="color: rgb(128, 128, 128); font-family: Courier New;">shredder $((sliceOffset*112*</span><code style="color: rgb(128, 128, 128); font-family: Courier New;">(246+2)*8</code><span style="color: rgb(128, 128, 128); font-family: Courier New;">)) $((1*112*</span><code style="color: rgb(128, 128, 128); font-family: Courier New;">(246+2)*8</code><span style="color: rgb(128, 128, 128); font-family: Courier New;">))
$((111*112*</span><code style="color: rgb(128, 128, 128); font-family: Courier New;">(246+2)*8</code><span style="color: rgb(128, 128, 128); font-family: Courier New;">)) <
</span><code style="color: rgb(128, 128, 128); font-family: Courier New;">dwi_ODFs.Bdouble</code><span style="color: rgb(128, 128, 128); font-family: Courier New;"> > cor_</span><code style="color: rgb(128, 128, 128); font-family: Courier New;">dwi_ODFs.Bdouble</code><br style="color: rgb(128, 128, 128); font-family: Courier New;">
<br>
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.<br>
<br style="color: rgb(128, 128, 128); font-family: Courier New;">
<span style="color: rgb(128, 128, 128); font-family: Courier New;"><span style="color: rgb(0, 128, 0);"># plot as usual, but remember to update -projection so that the ODFs are being viewed from the correct direction!</span></span><br style="color: rgb(128, 128, 128); font-family: Courier New;">
<span style="color: rgb(128, 128, 128); font-family: Courier New;">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</span><br style="color: rgb(128, 128, 128); font-family: Courier New;">
<br style="color: rgb(128, 128, 128); font-family: Courier New;">
<span style="color: rgb(128, 128, 128); font-family: Courier New;">convert -depth 8 -size 3584x1600 cor_dwi_ODFs.rgb cor_dwi_ODFs.png</span><br>
<br>
<code><span style="font-family: Tahoma;">The procedure is the same for the sagittal view:</span><br>
<br style="color: rgb(0, 128, 0);">
</code><span style="color: rgb(0, 128, 0); font-family: Courier New;"># sagittal image (slice 61) - read 61st element of each axial row of data</span><br style="color: rgb(128, 128, 128); font-family: Courier New;">
<span style="color: rgb(128, 128, 128); font-family: Courier New;">sliceOffset=60</span><br style="color: rgb(128, 128, 128); font-family: Courier New;">
<span style="color: rgb(128, 128, 128); font-family: Courier New;">shredder $((sliceOffset*4)) $((1*4)) $((111*4)) < fa.img > sag_fa.Bfloat</span><br style="color: rgb(128, 128, 128); font-family: Courier New;">
<span style="color: rgb(128, 128, 128); font-family: Courier New;">shredder $((sliceOffset*</span><code style="color: rgb(128, 128, 128); font-family: Courier New;">(246+2)*8</code><span style="color: rgb(128, 128, 128); font-family: Courier New;">)) $((1*</span><code style="color: rgb(128, 128, 128); font-family: Courier New;">(246+2)*8</code><span style="color: rgb(128, 128, 128); font-family: Courier New;">))
$((111*</span><code style="color: rgb(128, 128, 128); font-family: Courier New;">(246+2)*8</code><span style="color: rgb(128, 128, 128); font-family: Courier New;">)) <
</span><code style="color: rgb(128, 128, 128); font-family: Courier New;">dwi_ODFs.Bdouble</code><span style="color: rgb(128, 128, 128); font-family: Courier New;"> > sag_</span><code style="color: rgb(128, 128, 128); font-family: Courier New;">dwi_ODFs.Bdouble</code><br style="color: rgb(128, 128, 128); font-family: Courier New;">
<br>
<span style="font-family: Tahoma;">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.</span><br>
<br style="color: rgb(128, 128, 128); font-family: Courier New;">
<span style="color: rgb(128, 128, 128); font-family: Courier New;"><span style="color: rgb(0, 128, 0);"># again, remember to update -projection so that the ODFs are being viewed from the correct direction!</span></span><br style="color: rgb(128, 128, 128); font-family: Courier New;">
<code style="color: rgb(128, 128, 128); font-family: Courier New;">sfplot -inputmodel rbf -rbfpointset 246 -rbfsigma 0.2618 -xsize 50 -ysize 112 -minifigsize 30 30 -minifigseparation 2 2 -minmaxnorm -dircolcode -projection 3 -1 -backdrop
</code><span style="color: rgb(128, 128, 128); font-family: Courier New;">sag_fa.Bfloat</span><code style="color: rgb(128, 128, 128); font-family: Courier New;"> <
</code><span style="color: rgb(128, 128, 128); font-family: Courier New;">sag_</span><code style="color: rgb(128, 128, 128); font-family: Courier New;">dwi_ODFs.Bdouble</code><code style="color: rgb(128, 128, 128); font-family: Courier New;"> > sag_dwi_ODFs.rgb</code><br style="color: rgb(128, 128, 128); font-family: Courier New;">
<br style="color: rgb(128, 128, 128); font-family: Courier New;">
<span style="color: rgb(128, 128, 128); font-family: Courier New;">convert -depth 8 -size 3584x1600 sag_dwi_ODFs.rgb sag_dwi_ODFs.png</span><br>
<br>
Hope that helps.<br>
<br>
Kiran<br>
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