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SPM Home

SPM  November 2011

SPM November 2011

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Subject:

From:

John Ashburner <[log in to unmask]>

Reply-To:

John Ashburner <[log in to unmask]>

Date:

Fri, 25 Nov 2011 20:50:04 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (202 lines)

On the user interface for the segmentation, the default tissue
probability maps for GM, WM and CSF should already be defined.  If you
enter your own TPM, but in the wrong order, I think the main effect
will be that your GM is c3 and your CSF is c1.  Depending on your SPM
version, there may also be other subtle differences.

To double check the effects, you could segment one image with the
tissues specified in the right order to see what the effects are.

Best regards,
-John

On 24 November 2011 17:31, Marouane Nassim
<[log in to unmask]> wrote:
> 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
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> 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
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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
> 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)
> --------------------------------------------------
>
>
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