hello everyone
During the segment ( normalisation) is it important to enter the 3 tissue probablity map in this order ( Grey, white and csf ) ? , i did my preprocessing then i notice the order of my tissue was (cfs, grey and white), Is that a problem ?
Thank you
Marouane Nassim,B. Eng, Msc
Centre de recherche du CHU Ste-Justine
3175 Côte-Sainte-Catherine
Bloc 8, 2ième étage, bureau 2806
Montréal, Québec, Canada, H3T 1C5
Tél./phone: 514-345-4931, ext. 4046 ou 5702
Fax: 514-345-4801
email: [log in to unmask]
________________________________
From: SPM (Statistical Parametric Mapping) [[log in to unmask]] on behalf of MCLAREN, Donald [[log in to unmask]]
Sent: November 24, 2011 12:13 PM
To: [log in to unmask]
Subject: Re: [SPM] 回复:Re: [SPM] How to save the calculated img and hdr files
I forgot about that issue.
I usually also change Vo.dt(1) as well.
The available values are the numbers after the equal signs: uint8=2; int16=4; int32=8; float32=16; float64=64
The best practice would seem to be remove Vo.pinfo and change Vo.dt(1). One word of caution, if you need the values to be unscaled (e.g. you need a value of exactly 1 and you know your value is exactly 1), then you want to make sure you set pinfo(1) to be 1. If you don't care about the scaling, then you let the program set it.
A further word of caution, if you have values outside of the range of the datatype, it will be truncated. For example, if dt(1)=2 and pinfo(1)=1, then a value of 300 will be converted to a value of 255 or 256 -- this would be bad.
Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Office: (773) 406-2464
=====================
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.
On Thu, Nov 24, 2011 at 7:08 AM, CARLES M. FALCON FALCON <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Dear Ce,
you can use
V0=rmfield(V0,'pinfo')
before callin spm_write_vol
This removes pinfo from V0 structure. When pinfo is not defined, spm_write_vols calculates the optimum scale value for the image data type and range.
If pinfo is set to 1, you are forcing that the scale factor being 1. In data type is integer and your real values are small, you will lose all the decimals.
Hope this helps
Carles
Ce Mo <[log in to unmask]<mailto:[log in to unmask]>> ha escrit:
Dear Bas,
Thank you for your insightful comments. The problem has been solved exactly the way you described. ^_^
However, I am quite curious about your suggestion here,
"Also make sure the scaling is not off when using spm_write_vol. In your
Vo handle, this is implicitely stored as the optimal intensity scaling
for your previous image, which might not be good for your new data."
I noticed that there is not an explicit parameter for that in the spm_write_vol function. So how do I turn on the scaling when using spm_write_vol?
Many thanks and best regards,
Ce
----- 原始邮件 -----
发件人:S.F.W. Neggers <[log in to unmask]<mailto:[log in to unmask]>>
收件人:[log in to unmask]<mailto:[log in to unmask]>
主题:Re: [SPM] How to save the calculated img and hdr files
日期:2011-11-23 18:47:15
what is 'Res'? It should be a string with full path to the image
(i.e.,something like Res='/home/ce/data/mydata.img'). Then you will find
your image in that folder.
Without a path I guess your image will end up in your current folder,
but i am not sure about that.
Also make sure the scaling is not off when using spm_write_vol. In your
Vo handle, this is implicitely stored as the optimal intensity scaling
for your previous image, which might not be good for your new data.
Otherwise your code looks good to me.
Good luck,
Bas
Op 23-11-11 11:53, Ce Mo schreef:
Dear all,
I have been trying to write a code to perform some calculation on two
beta imgs, but I don't know how to save the result/calculated img.
I called the function spm_write_vol as:
out = sc.*me; % target
Vo = spm_vol(char(Canonical));% For simplicity, apply the input elements
Vo.fname = Res; % change name
Vo = spm_write_vol(Vo,out); % Write output img
where out is the calculated img.
After that, Vo was saved in workspace but I could not save the out.img
or out.hdr in the current folder or anywhere.
Any ideas and comments would be greatly appreciated.
Many thanks and best regards,
Ce
--
--------------------------------------------------
Dr. S.F.W. Neggers
Division of Brain Research
Rudolf Magnus Institute for Neuroscience
Utrecht University Medical Center
Visiting : Heidelberglaan 100, 3584 CX Utrecht
Room B.01.1.03
Mail : Huispost B01.206, P.O. Box 85500
3508 GA Utrecht, the Netherlands
Tel : +31 (0)88 7559609<tel:%2B31%20%280%2988%207559609>
Fax : +31 (0)88 7555443<tel:%2B31%20%280%2988%207555443>
E-mail : [log in to unmask]<mailto:[log in to unmask]>
Web : http://www.neuromri.nl/people/bas-neggers
: http://www.neuralnavigator.com (CEO)
--------------------------------------------------
------------------------------------------------------------------------------
De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct
te informeren door het bericht te retourneren. Het Universitair Medisch
Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W.
(Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij
de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.
Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
------------------------------------------------------------------------------
This message may contain confidential information and is intended exclusively
for the addressee. If you receive this message unintentionally, please do not
use the contents but notify the sender immediately by return e-mail. University
Medical Center Utrecht is a legal person by public law and is registered at
the Chamber of Commerce for Midden-Nederland under no. 30244197.
Please consider the environment before printing this e-mail.
|