JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for SPM Archives

SPM Archives

SPM Archives













By Topic:










By Author:











Proportional Font



SPM Home

SPM Home

SPM  November 2011

SPM November 2011


Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password



Marouane Nassim <[log in to unmask]>


Marouane Nassim <[log in to unmask]>


Thu, 24 Nov 2011 17:31:15 +0000





text/plain (1 lines)

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


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


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


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."


&nbsp;I noticed that&nbsp;there is not an explicit parameter for that in the&nbsp;spm_write_vol function. So how do I turn&nbsp;on the scaling when using spm_write_vol?


Many thanks and best regards,

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 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,


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,




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.

Top of Message | Previous Page | Permalink

JiscMail Tools

RSS Feeds and Sharing

Advanced Options


June 2019
May 2019
April 2019
March 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007

JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager