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Dear Guillaume, Thank you for your answer. I know that handling .nii is not a problem. I use it also as a default. What I am asking is handling 4D files. And with "handling" I mean, than SPM input/output. So if I call spm_reslice, spm_realign or any other spm function, will they accept 4D file as an input and create also 4D file as an output if appropriate? Kind regards, 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] -----Original Message----- From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of Guillaume Flandin Sent: Thursday, May 09, 2013 7:43 PM To: [log in to unmask] Subject: Re: [SPM] SPM with 4D NIFTI 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