 |
 |
Hi, I also have another registration-related question in addition to my questions in the previous post. If I have already run a full-model at the lower level and want to change some aspects of my design and run a new model on the same data, I understand that I can avoid having to do preprocessing again by using the filtered_func data saved in the previous model. Is there a similar way in which I can tell FSL to read the registration values from the previous analysis rather than have to perform flirt again? Thanks Vinod -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Vinod Venkatraman Sent: Monday, July 23, 2007 7:47 PM To: [log in to unmask] Subject: Re: [FSL] Between-run motion estimation Hi Christian, Thanks for your quick response. Yes, your interpretation of my second question is right. I have 6 runs for each subject and am combining them at the second level to see activations for this subject. When you say check higher-level registration report, I am not sure what you are referring to. I have a folder called inputreg which has the overlap images and those look good to me. Also, I just specify stats+post-stats option for higher-level and the registration is turned off here. In my fsf file, I have "Set fmri(reg_yn) 0". Should this not be the case and should this be 1 instead? My assumption was that since all images are registered in the lower level to the standard space, there is no need to do run registration at the higher levels except apply the estimated transformation values to the statistical images in normal space. Is this correct? Also, I am not sure what do you mean by "look at the registration of the two example_funcs to each other". Are you referring to just overlaying them on each other to see if they match? I have tried to do this visually using fslview and there does seem to be some difference between the two images (esp when comparing run1 and run6). But I am not able to quantify this in some way or attribute it to poor registration. The summary of registration output from lower level look similar to me (see my related question below). And if it is indeed a registration issue, am not sure what I can do to improve it. Finally, how should one interpret the registration outputs from FSL systematically? Any help on this would be useful. I am not sure what the red areas represent in these outputs. Thanks once again Vinod -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Christian Beckmann Sent: Monday, July 23, 2007 6:38 PM To: [log in to unmask] Subject: Re: [FSL] Between-run motion estimation Hi you could quantify the difference between the two examplefund2std matrices using rmsdiff but I'm not sure that this gives you meaningful information. Is it the case that the runs were acquired immediately one after another? Then you could also look at the registration of the two example_funcs to each other. Wrt your second question I'm not sure what you mean by 'when combining across runs within each subject'. Is it the case that you find weird activations after performing a higher level fixed-effects/ mixed-effects analysis that are not part of any of the lower-level results? It is possible that mis-registration can cause such edge effects, its therefore important that you always carefully check the higher-level registration report. hope this helps Christian On 23 Jul 2007, at 22:56, Vinod Venkatraman wrote: > Hi, > > What is the best way to get an estimate of between-run motion when > running analysis in FSL? I understand that FSL performs motion > correction within run > (Mcflirt) using the middle volume of the each run as reference. And > since each run is independently registered to the standard space, I > suppose there is no need to do a between-run motion correction as in > other packages. > However, is it possible to still get an estimate of this value? My > suspicion is that this can be inferred by looking at the registration > outputs > (examplefunc2standard.mat) but am not sure what values to exactly use. > > Also, is it possible that between-run motion can cause some form of > mis-registration which could lead to some weird activations on and > around the ventricles, when combining across runs within each subject? > > Vinod ____ Christian F. Beckmann University Research Lecturer Oxford University Centre for Functional MRI of the Brain (FMRIB) John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK. [log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann tel: +44 1865 222551 fax: +44 1865 222717