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SPM  May 2013

SPM May 2013

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Subject:

Re: SPM with 4D NIFTI

From:

"MCLAREN, Donald" <[log in to unmask]>

Reply-To:

MCLAREN, Donald

Date:

Thu, 9 May 2013 15:09:13 -0400

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (137 lines)

All our code, peak_nii and gPPI included can handle .nii extensions or
be easily modified to handle them.


On Thu, May 9, 2013 at 2:45 PM, YAN Chao-Gan <[log in to unmask]> wrote:
> Hi Guillaume,
>
> REST changed the default format to .nii half a year ago. I feel a single
> .nii file is better than .img/.hdr pairs.
>
> Thus I vote changing the default setting to .nii for SPM: +1. :)
>
> Best,
>
> Chao-Gan
>
>
> On Thu, May 9, 2013 at 2:43 PM, Guillaume Flandin <[log in to unmask]>
> wrote:
>>
>> Dear Tibor,
>>
>> just to add that you can find more details here:
>>   http://en.wikibooks.org/wiki/SPM/Working_with_4D_data
>>
>> In SPM12, you can enter Inf in the frame entry instead of 1:999...
>> You also have the option to use single (.nii) instead of dual
>> (.hdr/.img) file storage in global defaults:
>>   defaults.images.format  = 'img'; % options: 'img', 'nii'
>>
>> While I am in favour of using single NIfTI files (.nii) throughout SPM
>> as default, you might sometimes observe slowdowns when using 4D files
>> (as compared to 3D files).
>> I'd be happy to hear feedbacks from those of you who use 4D files
>> routinely. I'd also welcome views on the change to have .nii files as
>> default: will it affect your in-house scripts if GLM outputs are saved
>> with (3D) single file storage (beta_0001.nii, con_0001.nii, mask.nii,
>> etc)?
>>
>> Best regards,
>> Guillaume.
>>
>>
>>
>> On 09/05/13 18:23, MCLAREN, Donald wrote:
>> > Just select all the frames you want in the analysis or processing. If
>> > the input is 4D then then the output will be 4D - at least for all the
>> > things that I have tried.
>> >
>> > Best Regards, Donald McLaren
>> > =================
>> > D.G. McLaren, Ph.D.
>> > Research Fellow, Department of Neurology, Massachusetts General Hospital
>> > and
>> > Harvard Medical School
>> > Postdoctoral Research Fellow, GRECC, Bedford VA
>> > Website: http://www.martinos.org/~mclaren
>> > Office: (773) 406-2464
>> > =====================
>> > This e-mail contains CONFIDENTIAL INFORMATION which may contain
>> > PROTECTED
>> > HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
>> > 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, May 9, 2013 at 1:10 PM, Tibor Auer
>> > <[log in to unmask]> wrote:
>> >> Dear SPMers,
>> >>
>> >>
>> >>
>> >> Is there an easy way to make SPM read and write 4D NIFTI as default
>> >> during
>> >> analysis, or one has to “tweak” the code?
>> >>
>> >>
>> >>
>> >> I am aware of SPM tools for reading and writing 4D NIFTI, but then it
>> >> means
>> >> that I have to convert files manually.
>> >>
>> >>
>> >>
>> >> Cheers,
>> >>
>> >>
>> >>
>> >> Auer, Tibor M.D. Ph.D.
>> >>
>> >> MRC Cognition and Brain Sciences Unit
>> >> 15 Chaucer Road
>> >> Cambridge
>> >> CB2 7EF
>> >>
>> >> United Kingdom
>> >>
>> >> Phone/Work: +44-(0)1223-355294 (ext. 869)
>> >>
>> >> Mail: [log in to unmask]
>> >>
>> >>
>> >
>>
>> --
>> Guillaume Flandin, PhD
>> Wellcome Trust Centre for Neuroimaging
>> University College London
>> 12 Queen Square
>> London WC1N 3BG
>
>
>
>
> --
> Chao-Gan YAN, Ph.D.
> Research Scientist
> The Nathan Kline Institute for Psychiatric Research, 140 Old Orangeburg
> Road, Orangeburg, NY 10962
> Center for the Developing Brain, Child Mind Institute, 445 Park Avenue, New
> York, NY 10022
> The Phyllis Green and Randolph Cowen Institute for Pediatric Neuroscience,
> New York University Child Study Center, New York, NY 10016
> http://www.restfmri.net/forum/yanchaogan
> http://scholar.google.com/citations?user=lJQ9B58AAAAJ&hl=en

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