These neurons were quite dusty: http://brainvis.wustl.edu/help/pals_volume_normalization/flirt_normalization_pals.html
On Dec 26, 2012, at 3:20 PM, Timothy Coalson <tsc...@mst.edu> wrote: > flirt does not use the nifti origin, I think this may be the cause of your > problems. I wrote a utility to convert between simple coordinate to > coordinate matrices and the matrices flirt expects (and another convention or > two specific to 4dfp). You probably won't have it unless you have a very > recent version of the 4dfp suite (look for the source folder/executable > "aff_conv" if you do). > > To be precise, flirt uses the pixdim field of nifti for the spacing, with an > origin at voxel (0, 0, 0), that is, corner of the volume. However, it also > checks for the sform having positive determinant, and if so, does an x-flip > of the coordinate system (that is, negates the x spacing, and puts the origin > at voxel (X, 0, 0) where X is the largest possible value of the first index). > > In short, yes it should be simple, but it isn't. I actually don't know of a > volume transform/resampling utility that works correctly with an > unadulterated coordinate to coordinate transform. > > Tim > > On Wed, Dec 26, 2012 at 12:16 PM, Colin Reveley <cm...@sussex.ac.uk> wrote: > thanks donna - I know that. > > I'm talking about volumes and surfaces that are already aigned, and humming > nicely. > > I want to apply an arbitrary linear operation to the volume (actuslly just > two rotations, but it shoould generalise presumably) and the surface, and > have them stay linked. > > so, turn it upside down. double it's size. > > one matrix. two things (MRI data, and surface representations of exactly that > data) that are equivalent in space under any transform I care to apply. > > > > On 26 December 2012 18:00, <caret-users-requ...@brainvis.wustl.edu> wrote: > Send caret-users mailing list submissions to > caret-users@brainvis.wustl.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://brainvis.wustl.edu/mailman/listinfo/caret-users > or, via email, send a message with subject or body 'help' to > caret-users-requ...@brainvis.wustl.edu > > You can reach the person managing the list at > caret-users-ow...@brainvis.wustl.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of caret-users digest..." > > Today's Topics: > > 1. Re: transform surf and vol (Donna Dierker) > > > ---------- Forwarded message ---------- > From: Donna Dierker <donna.dier...@sbcglobal.net> > To: "Caret, SureFit, and SuMS software users" <caret-users@brainvis.wustl.edu> > Cc: > Date: Tue, 25 Dec 2012 15:31:48 -0600 > Subject: Re: [caret-users] transform surf and vol > If you import a Freesurfer surface into Caret, it won't align with the volume > in mri/orig.mgz until you apply an offset transformation defined by something > like mri_info -cras (I forget the exact command). Depending on which surface > you apply that transformation -- before or after cras offset -- you could get > the behavior you describe. > > > On Dec 24, 2012, at 7:51 PM, Colin Reveley wrote: > > > Hey, merry christmas. > > > > I have a surface. and a volume. they are in register in caret. the volume > > has an origin reported in the nifti header. > > > > If I apply a rigid body transform to both, they are both rotated the way I > > want (the way I want is so that the surface, and MR data in the slice plane > > as some microscope slides of the sample) but the surface is no longer in > > register with the volume. > > > > the rotations are right. but the translations aren't (there aren't any > > translations intended actually) > > > > I can > > > > a) manually translate the surface around in caret till it roughly fits > > (which I did, it's fine for now) > > b) adjust the origin of the nifti (the origin isn't changed by applying the > > transform with flirt) > > > > or I guess c) adjust something in the surface header. couldn't see what. > > > > It occurred to me to treat the original volume origin as a vector and apply > > the transform to it, then set the origin of the rotated volume to those > > values. > > > > Probably that would work. But it's a bit too much linear algebra for me. > > > > Moving on from the obvious fact that I'm not that bright, surely doing > > exactly this kind of thing ought to be pretty easy? > > > > > > _______________________________________________ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
