[Camino-users] schemefile generation -problem is solved

[stefania oliviero]

Hi Matt

thanks a lot for your suggestion.


Cheers,

Stefania

________________________________
Da: Hall, Matt <matt.hall at ucl.ac.uk>
Inviato: lunedì 3 aprile 2017 14.42.23
A: stefania oliviero; camino-users at www.nitrc.org
Oggetto: RE: [Camino-users] schemefile generation -problem is solved

Hi Stephania,

The drawcrosssection switch as you’ve used it there only works with the distributed radius substrates. The fixed radius substrates are so simple that we didn’t think anyone would need it! With a single radius, hexagonal packing, and a given cylinder separation the substrate is pretty easy to visualise with something like matlab – you just get a cylinder of radius r at each corner of repeating equilateral triangles with sides length 2R.

Cheers,
Matt.

From: camino-users-bounces at www.nitrc.org [mailto:camino-users-bounces at www.nitrc.org] On Behalf Of stefania oliviero
Sent: 03 April 2017 13:37
To: camino-users at www.nitrc.org
Subject: Re: [Camino-users] schemefile generation -problem is solved

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<mailto:camino-users-bounces at www.nitrc.org> <camino-users-bounces at www.nitrc.org<mailto:camino-users-bounces at www.nitrc.org>> per conto di stefania oliviero <stefania.oliviero at hotmail.it<mailto:stefania.oliviero at hotmail.it>>
Inviato: lunedì 24 marzo 2014 10.35.24
A: Ferizi, Uran; camino-users at www.nitrc.org<mailto: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<mailto:uran.ferizi.10 at ucl.ac.uk>
To: stefania.oliviero at hotmail.it<mailto:stefania.oliviero at hotmail.it>; camino-users at www.nitrc.org<mailto: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<mailto:camino-users-bounces at www.nitrc.org> <camino-users-bounces at www.nitrc.org<mailto:camino-users-bounces at www.nitrc.org>> on behalf of stefania oliviero <stefania.oliviero at hotmail.it<mailto:stefania.oliviero at hotmail.it>>
Sent: 24 March 2014 7:35 AM
To: camino-users at www.nitrc.org<mailto: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
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