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SPM  November 2011

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Subject:

From:

Marouane Nassim <[log in to unmask]>

Reply-To:

Marouane Nassim <[log in to unmask]>

Date:

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

Content-Type:

text/plain

Parts/Attachments:

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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

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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,

&nbsp;



Thank you for your insightful comments. The problem has been solved exactly the way you described. ^_^

&nbsp;



However, I am quite curious about your suggestion here,

&nbsp;



"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;

&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?

&nbsp;



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,



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

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Mail : Huispost B01.206, P.O. Box 85500

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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)

--------------------------------------------------





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