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Dear Randy, The UI should be able to deal with this in SPM8. We are generally much more motivated to fix SPM8 problems than SPM2 problems, so if it doesn't work, then it soon should. Best regards, -John On Monday 15 December 2008 03:02, Randolph Andrews wrote: > No frames displayed in the GUI, so no selection option was available (also > tested a re-process through 3rd party software; worked with spatnorm just > fine as before). SPM2 is getting a bit stale... rather than have someone > chase down code to fix this and since I have a work-around at this time, > it's no big deal. > On the other hand, does this GUI function work in SPM8 (or 8b)? I plan to > migrate to SPM8 in a few months to make use of the topological false > discovery rate feature anyway. I can provide a sample 4D (4D PET and > target MRI) for testing or for any errors on my side for SPM2 (or for SPM8) > to see if the answer is no (or if anyone's interested). > -Randy > > > "Far better an approximate answer to the right question, which is often > vague, than an exact answer to the wrong question, which can always be made > precise" John W. Tukey, Ann. Math. Stat., vol. 33, p. 13, 1962 > > --- On Thu, 12/11/08, John Ashburner <[log in to unmask]> wrote: > > From: John Ashburner <[log in to unmask]> > Subject: Re: [SPM] 4D coreg solution (4D spatnorm works) > To: "Randolph Andrews" <[log in to unmask]>, [log in to unmask] > Date: Thursday, December 11, 2008, 11:23 AM > > First of all, I should point out to anyone on the list who may read these > emails, that this query relates to SPM2. > > Did you select all frames of the uncoregistered 4D file, or just the file? > If you just select the file, SPM will consider it as a single 3D volume - > rather than a series of 3D volumes. > > Best regards, > -John > > On Wednesday 10 December 2008 21:26, Randolph Andrews wrote: > > Dear List, > > > > On Monday I posted a question concerning the application of previous > > transforms on 4D images (see appended). After searching the archives, I > > found John's excellent post concerning changing the spm_default.m > > "multivol > > > = true" which saves me ONE multivolume parse/operation/recombine > > step. > > > Using 3rd party software I was able to construct a coregistered > > multivolume > > > file. THEN, after changing the spm_default.m, I was able to spatially > > normalize my coregistered "sum" image (works fine) and when I > > selected > > > "Write Normalised Only" on the 3rd-party 4D file, a tidy list of > > individual > > > volumes came up in the GUI and I selected them in order, hit > > "Done" and SPM > > > wrote out a perfectly servicable 4D, spatially normalised file. > > > > Thinking "excellent... lets see if I can cut out the 3rd-party > > step", I > > > started from scratch, and I coregistered "sum" image in SPM > > afresh. During > > > the initial interaction with the GUI, I selected "Other Images" > > "the > > uncoregistered 4D file", hit "Done". Unfortunately, as > > happened on Monday, > > > SPM only wrote the first volume (1 of 21, pretty much useless on it own). > > > > OK, no good. Lets try applying the transform after the fact... > > > > Started from scratch again, but this time I only coregistered and wrote > > out > > > the "sum" image. With the *.mat file in place, I restarted the > > SPM > > > coregister routine again and selected "Reslice Only" > > > "Space defining > > > image" > > > > > "coregistered-sum-PET", thinking the change in > > spm_default.m would engage > > > as it had in the spatnorm test I'd run earlier and I'd see a > > similar list > > > of individual volumes to select. No such luck. Also, only the 1st volume > > wrote out again. > > > > While I actually have a solution I could live with (albeit still a little > > clunky), I'd really like to avoid the 3rd party solution: > > > > ---Is there some reason why "multivol = true" works with spatial > > writing > > > step and not the coreg writing step? > > ---Is there something in the spm_coreg.m I could/should change? > > > > Thanks in advance, > > > > Randy > > > > > > PS. Alexander: Thank you for your speedy reply on Monday. > > > > > > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > > > > John's 2005 post > > > > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > > > > Subject: Re: dynamic spm2 analyze format > > From: John Ashburner <[log in to unmask]> > > Reply-To: John Ashburner <[log in to unmask]> > > Date: Wed, 12 Oct 2005 10:42:47 +0100 > > Content-Type: text/plain > > > > > I have a question about an Analyze format and SPM's capability to > > handle > > > > it. > > > > > > Does Analyze allow us to store 'dynamic' images (images at > > different time > > > > points) in a single file? Can SPM2 handle this kind of file, > > especially > > > > in the co-registration or spatial normalization? > > > > > > We are having a need to register and warp dynamic PET images using > > SPM2. > > > In principle, SPM2 can handle 4D volumes, although you need to set the > > defaults.analyze.multivol field to enable this. This is either by > > editing spm_defaults.m, or by starting up SPM and typing.. > > > > global defaults > > defaults.analyze.multivol = true; > > > > SPM2 has a few slight problems in terms of file selection though, but > > these > > > should be resolved in spm5b. In SPM5b, when selecting images, you would > > change the field that normally says "1", to the range of volume > > numbers you > > > want (e.g. "1:30"). > > > > Reading the image headers in order to obtain the number of volumes has a > > bit of an impact on speed, so you don't by default have the option to > > select individual volumes. > > > > Best regards, > > -John > > > > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > > > > My Monday post and Alexander's reply > > > > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > > > > RE: [SPM] Coregistration (reslice only?) of multiframe image after > > summed- frame image works OK > > Monday, December 8, 2008 9:40 PM > > From: "Hammers, Alexander" > > <[log in to unmask]>Add sender > > > to Contacts To: "Randolph Andrews" > > <[log in to unmask]>, > > > [log in to unmask] > > > > Dear Randolph, > > > > > > I'm afraid when we did this we did it to individual frames, too. Maybe > > you can script this to be ready before this year's Christmas? > > > > Have you thought of another much more pain-free option - work in PET > > space and coregister the MRI to your summed PET image? > > > > Good luck & hope this helps, > > > > Alexander > > PS: Incidentally, you should normally weigh your frames for your summed > > image depending on frame length and number of events - but for a simple > > task like co-registration your simple sum will work for most tracers > > with any cortical signal at all. > > > > > > > > > > -----Original Message----- > > From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] > > On Behalf Of Randolph Andrews > > Sent: 08 December 2008 21:03 > > To: [log in to unmask] > > Subject: [SPM] Coregistration (reslice only?) of multiframe image after > > summed-frame image works OK > > > > I'm very used to working with static images (FDG using SPM96, SPM99, > > SPM2) > > > but I now need to coregister dynamic images (21 frames) to a subject's > > MRI. > > > The early frames don't have a whole lot of information, so I've > > summed all > > > frames into a sngle image, and the coregistration works just fine on > > that. > > > > I originally thought I could coregister and reslice the summed image and > > when the GUI prompted for "other images", I'd just select > > the dynamic image > > > and SPM would use the transform obtained from the first coregistation and > > reslice all 21 frames of 2nd image. > > > > It appears to only reslice the 1st frame of the dynamic image (not a > > whole lot of use by itself). I've seen some earlier posts (4D image) > > that suggested I parse the dynamic image frame-by-frame, but I have 96 > > of these, and I'd like to get this coregistration step done before > > Christmas > > > (of next year). > > > > Using "Reslice Only" prompts me to select "Space defining > > image, subj 1". > > > I've tried both the r(summed image) and the MRI, and I still only get > > the > > > 1st frame. > > > > Help?