No support for spm ecat import and imcalc ?

[Pankaj Singh]

Hi,

I could not find ecat import and imcalc utility in spm interface? Is it available?
If it is not there then is it that people generally do not use them? In that case what are the alternatives?

Regards,
Pankaj

[Pankaj Singh]

My requirement is as below :
1) Convert ecat to nii (was previously using ecat  from spm util)
2) use spm realign
3) do basic image arithmetic. (was previously using imcalc from spm)

Please suggest the alternatives.

[cindee]

Hi Pankaj,

Have you tried nibabel ?
http://nipy.sourceforge.net/nibabel/

It allows you to read in ecat images and save them to nifit format...

you also have basic access to the data array...

import nibabel.ecat as ecat

img = ecat.load('someimage.v')

you have access to frames and header info, and mlist

--Cindee

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Cindee Madison
Jagust Lab
UC Berkeley
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[Pankaj Singh]

Hi Cindee

Thanks. But I want to conver ecat to nii so that I can use it in other flows. is there any utility in nibable to do so?

Regards,
Pankaj

[cindee]

I have some code that should work for you...I should have time to put it up on github gist later tonight or tmr am?

Ill plan to add this as an example in nibabel...should have done this long ago...

--Cindee

[cindee]

This is quick,  but hopefully helps

https://gist.github.com/cindeem/7347843

--C