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featregapply ;-) On 12 May 2011, at 13:25, Cinly Ooi wrote: > Dear All, > > Thank you for continuing to provide quick (and accurate) responses to all my questions. > > I am in the process of finalizing the feat scripts for a project and needed the cope*.nii.gz and varcope*.nii.gz in standard space (AAL template space, i.e. 91x109x91...) to extract statistics value for individual AAL region. > > Reading http://www.fmrib.ox.ac.uk/fsl/feat5/output.html says I can get them in standard space in reg_standard directory > > An old posting (2007) found in http://www.biac.duke.edu/forums/topic.asp?TOPIC_ID=1062, says reg_standard is created by second level. I tried it and it works. I chosen the stats to be single group average. I was wondering whether is there an option in first level analysis that can do it. > > My question are: > > (1) Is it possible to generate reg_standard in 'First Level Analysis' easily? > > (2) To create all the standardspace images quickly, I plan to run as many second level analysis as possible. Ideally, this means one per subject. > > I do not have a SGE machine setup unfortunately > > However, 'Higher Level' analysis UI requires me to put in two datasets, regardless of whether is it 'Lower level FEAT directory' or 'cope files'. As I only need reg_standard directories inside individual subject's directory, can I leave the second FEAT directory/cope file blank? > > I tried it. As expected, I got failure at 'Higher Level Input Files Preparation', but the reg_standard/stats/cope*.nii.gz and varcope*.nii.gz were generated for the first FEAT directory. Can someone confirm that the cope and varcope files are good, i.e. I can use it to extract statistics? What I am worry about is that these are intermediate results and a process will convert them to the final results later. However, looking at how FEAT uses temporary files to hold intermediate data, I do not think they are temporary results and therefore they are OK. Am I correct? > > Many thanks in advance and hope to hear from you all soon. > > Best Regards, > Cinly > > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------