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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