[Camino-users] sfplot warning/error

[Zhuang Song]

Hi Kiran and Matt,

Thank you both for the thoughts and suggestions. To create the FA map, I
used the scripts in the online Tutorial for DTI (
http://cmic.cs.ucl.ac.uk/camino//index.php?n=Tutorials.DTI):

for PROG in fa md; do
  cat dt.Bdouble | ${PROG} | voxel2image -outputroot ${PROG} -header
4Ddwi_b1000.nii.gz

done

This script actually generated FA map in NIFTI format. Since I thought
fa.img was in ANALYZE format as it looks like, I converted the FA map in
NIFTI to ANALYZE format and then did the 'split'. It was due to a confusion
of the format of fa.img.  This became clear to me after I ran the command
suggest by Kiran:  fa < dwi.Bfloat > fa.img, because there was no fa.hdr in
the output as in the ANALYZE format.

However there is still a problem with 'split' after using Kiran's script to
generate fa.img. By running split -b $((112*112*8)) fa.img
splitBrain/fa_slice (for the example human brain data in the tutorial), the
total slice number of the FA map become 104, which is supposed to be 50.
What would be the problem now?

Thanks for giving the scripts to display ODF in three views. It doesn't
looks straightforward and I will test it carefully later. I will keep you
updated.

Many thanks,
Zhuang


On Tue, Aug 14, 2012 at 8:37 AM, Seunarine, Kiran <k.seunarine at ucl.ac.uk>wrote:

>  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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