[Camino-users] schemefile generation -problem is solved

[stefania oliviero]

Hi All,
I have a question about the option drawncrosssection of command datasynth.


If I run the command:


datasynth -walkers ${WALKERS} -tmax ${TIMESTEPS} -substrate cylinder -packing hex -cylinderrad 1E-6 -cylindersep 2.1E-6 -voxels 1 -p 0.0 -schemefile ${SCHEMEFILE} -initial uniform -diffusivity ${DIFF} -substrateinfo -drawcrosssection ${FNAME}.gray > ${OUTPUTDIR}/${FNAME}.Bfloat 2> ${FNAME}.txt


I do not obtain any file .gray

while, if I change the substrate and run the command:


datasynth -walkers ${WALKERS} -tmax ${TIMESTEPS} -geometry inflammation -numcylinders ${NUMCYL} -p 0 -initial uniform -seed ${INT_rnd} -voxels 1 -increments 1 -separateruns -latticesize ${LATSIZE} -schemefile ${SCHEMEFILE} -gamma ${GAMA} ${GAMB} -diffusivity ${DIFF} -substrateinfo -drawcrosssection ${FNAME}.gray > ${OUTPUTDIR}/${FNAME} 2> ${FNAME}.txt


I obtain a file .gray


What is the problem in the first command?

Does option drawncrossssection work only with inflammation substrate?




Thanks a lot

Cheers

Stefania Oliviero
ITAB, Università degli Studi G. d'Annunzio di Chieti

________________________________
Da: camino-users-bounces at www.nitrc.org <camino-users-bounces at www.nitrc.org> per conto di stefania oliviero <stefania.oliviero at hotmail.it>
Inviato: lunedì 24 marzo 2014 10.35.24
A: Ferizi, Uran; camino-users at www.nitrc.org
Oggetto: Re: [Camino-users] schemefile generation -problem is solved

Hi Uran,
Thank you so much!
I did not know Stejskal-Tanner version of schemefile and now the problem is solved.

Cheers
Stefania Oliviero
________________________________
From: uran.ferizi.10 at ucl.ac.uk
To: stefania.oliviero at hotmail.it; camino-users at www.nitrc.org
Subject: RE: [Camino-users] schemefile generation
Date: Mon, 24 Mar 2014 08:39:47 +0000

Hello Stefania,


If you asked about how to write a Stejskal-Tanner scheme file, which is a text file, you could use Matlab.


After constructing the matrix, e.g.:
ST_scheme=[directions; |G|;  DELTA; delta TE];
you can write it out via:


scheme_str=strcat('data.scheme');
dlmwrite(scheme_str, ST_scheme, 'delimiter', ' ', 'precision', '%.6f');
% write first line
dlmwrite('output.txt', 'VERSION: STEJSKALTANNER', 'delimiter', '');
% append rest of file
dlmwrite('output.txt', fileread(scheme_str), '-append', 'delimiter', '');
% overwrite on original file
movefile('output.txt', scheme_str);




________________________________
From: camino-users-bounces at www.nitrc.org <camino-users-bounces at www.nitrc.org> on behalf of stefania oliviero <stefania.oliviero at hotmail.it>
Sent: 24 March 2014 7:35 AM
To: camino-users at www.nitrc.org
Subject: [Camino-users] schemefile generation

Hi All,
I have a question about the generation of a schemefile. I have an acquisition scheme like this:

nx ny nz  delta  DELTA  G      TE

0   0   0     0       0          0     30
5   10 0     8       20        80   50
...

with nx, ny and nz as gradient directions.
How can I report all these information in a scheme file? I would like to explicit in the file.scheme the values of delta, DELTA, G and TE. Which schemefile version can I use, please?
The only scheme file version explained in the DTI tutorial is the BVECTOR one.

VERSION: BVECTOR
nx_1 ny_1 nz_1 b1

Thanks a lot
Cheers

Stefania Oliviero
Università degli Studi di Napoli Federico II
ITAB, Università degli Studi G. d'Annunzio di Chieti
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.nitrc.org/pipermail/camino-users/attachments/20170403/bc28485b/attachment.html>