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SPM  November 2011

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Subject:

Re: 回复:Re: [SPM] 回复:Re:_[SPM] How to save the calculated img and hdr files

From:

"CARLES M. FALCON FALCON" <[log in to unmask]>

Reply-To:

CARLES M. FALCON FALCON

Date:

Mon, 28 Nov 2011 11:24:52 +0100

Content-Type:

text/plain

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text/plain (182 lines)

Hi Ce,
in my opinion the easier is to use spm_imcalc. The only is if you need  
to loop the process or if you don't want to write a very complicated  
equation in case of using a lot of images at once. spm_imcalc works in  
real world so it takes into account spatial position and geometric  
charactesitics of images. If you uses a matrix-wise approach you have  
to ensure that voxels being in the same spatial postion have the same  
matrix coordinates in all images (all images have the same geometrical  
'prescription', that is they share matrix characteristics and the  
(4x4) mat field). spm_imcalc can be also used in a batch/script mode.  
Nevertheless it is important to feel confident with what your are  
doing. If you think that some hidden process in spm_imcalc could  
result in losing of important information you could run your own  
scripts and check for differences.
Best wishes
Carles

Ce Mo <[log in to unmask]> ha escrit:

> Dear&nbsp;Carles and Bas,
> &nbsp;
> Thank you for your insightful&nbsp;advice. I really appreciate it!
> &nbsp;
> However, I still have one more&nbsp;question. When performing image  
> calculation, which&nbsp;might be the better choice, making direct  
> call to function spm_imcalc and perform the calculation in its  
> framework, or do the matrix element wise calculation myself? The  
> latter one seems much more straightforward but the concern is that I  
> am so familiar with some masking or interpolation that&nbsp;are  
> encapsulated in spm_imcalc, which&nbsp;might be tricky and I don't  
> know whether I would&nbsp;lose some vital information if I do the  
> calculation myself.&nbsp; Any ideas?
> &nbsp;
> Many thanks and best regards,
> &nbsp;
> Sinerely yours
> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Ce
>
> ----- 原始邮件 -----
> 发件人:CARLES M. FALCON FALCON <[log in to unmask]>
> 收件人:[log in to unmask]
> 主题:Re: [SPM] 回复:Re:_[SPM] How to save the calculated img and hdr files
> 日期:2011-11-24 21:08:14
>
> 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]> 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]>
>> 收件人:[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
>> Fax : +31 (0)88 7555443
>> E-mail : [log in to unmask]
>> Web : http://www.neuromri.nl/people/bas-neggers
>> : http://www.neuralnavigator.com (CEO)
>> --------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------------
>>
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>>
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>>
>> ------------------------------------------------------------------------------
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>

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