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Sounds good, though it's probably better to use example_func to register to the anatomical. If you've done registration inside FEAT you should find all the transforms you need in the .feat/reg directory. Cheers, Steve. On 17 May 2006, at 20:17, Martin M. Monti wrote: > Steve, > > my simple plan was the following: > > 1) Align filtered_func to the subject's anatomical via flirt > > 2) Register the mask (created in Standard space) to the individual > subject by using the inverse of highres2standard.mat , and use the > example_filtered_func as the reference. This way the mask is > registered to the functional (i.e. they both are registered to the > subject's anatomical) and the header of the mask is the same as the > functional. (at this point I'll use avwmeants to pull out > timecourses from that mask) > > [alternatively I could probably just apply to the 'standard' mask > the inverse of the example_func2standard.mat, but I have several > functionals and I'd like to concatenate them to then use once > avwmeants] > > Makes good sense? > > Cheers & thanks for the continuous support, > > Martin > > ----- Original Message ----- From: "Steve Smith" > <[log in to unmask]> > To: <[log in to unmask]> > Sent: Thursday, May 18, 2006 2:55 AM > Subject: Re: [FSL] filtered_func & Peri-Stimulus plot > > >> Hi, >> >> On 17 May 2006, at 18:13, Martin M. Monti wrote: >> >>> Mark, >>> >>> thank you, avwmeants works great! >>> Only one question: does the mask used have to be in the FOV of >>> the functional I'm pulling out the timecourses from? >>> >>> I.e. say I do: avwmeants -i filtered_func_data -o tseries.txt -m >>> Mask --showall >>> >>> Does 'Mask' have to have same FOV and voxel resolution as >>> filtered_func_data? >> >> Yes. >> >>> I presume I can use flirt on the mask with filtered_func_data as >>> a reference image to have them have these same header properties? >> >> Indeed, as long as you have an appropriate FLIRT transform file >> to tell it to apply to the mask. >> >> Cheers, Steve. >> >> >>> >>> Thank for the help, >>> >>> Martin >>> >>> ----- Original Message ----- From: "Mark Jenkinson" >>> <[log in to unmask]> >>> To: <[log in to unmask]> >>> Sent: Tuesday, May 16, 2006 6:36 AM >>> Subject: Re: [FSL] filtered_func & Peri-Stimulus plot >>> >>> >>>> Hi Martin, >>>> >>>> You can get individual time courses or averages using avwmeants >>>> (the output is in text form). This will let you process the >>>> values later >>>> in whatever way you want. >>>> >>>> You are correct about the filtered_func_data - it does not have >>>> registration applied to it (but is motion corrected). >>>> >>>> I'm not quite sure what is wrong with your Featquery, but your >>>> usage of avwroi is wrong, as you need to use voxel coordinates, >>>> not mm coordinates. All the voxel coordinates should be integers >>>> between 0 and N-1 (inclusive). Using -34 as a coordinate would be >>>> well outside the volume and hence not give you anything except >>>> zeros in the resulting output. >>>> >>>> All the best, >>>> Mark >>>> >>>> >>>> On 15 May 2006, at 19:42, Martin M. Monti wrote: >>>> >>>>> FSL masters, >>>>> >>>>> I have 2 ( somewhat unrelated questions) >>>>> >>>>> 1) the filtered_func_data: this is the data with all pre- >>>>> processing steps I asked for, EXCEPT for registration with the >>>>> High-res and MNI-Template? I'm trying a multi-voxel analysis >>>>> of my data and need to pull out time-courses for various >>>>> regions. Also, is there a way to pull out the time-courses >>>>> associated to EACH voxel within a mask? I know avwroi will >>>>> pull out one average from a given mask. Is there any pre- >>>>> compiled utility to pull out each and all the voxels from a >>>>> mask? >>>>> >>>>> 2) I tried featquery to get a peristimulus plot, but I get >>>>> more event plots than I actually have (i.e. 8 instead of 5!). >>>>> This is by selecting the filtered_func_data and clicking on >>>>> the PE/% signal change and peri-stimulus plot options (I use a >>>>> mask in MNI coordinated and use single-voxel coords). Indeed I >>>>> think I remember someone mentioning that FSL is left to >>>>> "guess" what an event is. Is there a way to instruct FSL as of >>>>> the timepoints that make an event? >>>>> Alternatively I was wondering whether I could just extract the >>>>> raw timecourse from the filtered_func_data using avwroi and >>>>> then manually create the plots (excel-style). Re this, one >>>>> thing I'm unclear about is, when the syntax requires size: is >>>>> that number of voxels or voxel size? I tried using 1 for all >>>>> dimensions (e.g. avwroi filtered_func_data TC_out -34 1 60 1 >>>>> 4 1) but i then couldn't open the image. By changing the 1s >>>>> to the voxel dimension I could successfully create a new >>>>> image. Is this correct? >>>>> >>>>> cheers >>>>> >>>>> Martin >>>>> >> >> >> --------------------------------------------------------------------- >> --- --- >> 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 >> --------------------------------------------------------------------- >> --- --- ------------------------------------------------------------------------ --- 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 ------------------------------------------------------------------------ ---