Hi everyone,
Just a quick word of warning (plus two follow-up questions): there are more
instances where your brain can get flipped. For example, I just regenerated my
surface, using the correct orientation, certain about that. If I then do
bbregister afterwards using the structural I convert back from the struct
freesurfer used to contruct the surface (001.mgz, so mri_convert 001.mgz
freesurferstruct.nii) like this
bbregister --mov freesurferstruct.nii --init-spm --reg someRegFile.dat --t1
Note: this should be perfect to start with. But, in contrast, it's flipped
again. Why? Because of the init-spm. If I use init-header (or use tksurfer to
generate the reg file) everything is fine, which makes kinda sense (I use a
converted freesurfer file) not quite (it is a nifti file which has the right
orientation in SPM viewer).
So why is this happening? Because of an incorrect/incomplete dicom conversion
by the SPM-tools, which causes it to lose crucial orientation information?
Moreover: is there an easy sanity check to see whether the orientation is right
now? I thought about superimposing the original structural, to see how it ends
up on the surface (should nicely follow the sulci/gyrii), but apparently there
is a strong gradient in there and it is quite dotted, so it ends up not showing
me all gyrii, just a subset, and a bit scattered. Is there a better way?
Thanks again, hope also this is useful for others,
best, Frank
----- "Dan Wakeman" <dgwake...@gmail.com> schreef:
> Van: "Dan Wakeman" <dgwake...@gmail.com>
> Aan: "F.T.M. Léoné (Frank)" <f.le...@donders.ru.nl>
> Verzonden: Donderdag 19 januari 2012 18:14:07
> Onderwerp: Re: [Freesurfer] Freesurfer flips brains?
>
> Hi Frank,
>
> If your problem is solved then it's fine. I didn't understand what
> you
> said, and I am not sure I still understand your hemisphere problems.
> Especially, because you cannot check the left right alignment (or
> even
> view any volume) in tksurfer.
>
> In general I would say it makes more sense to align your functional
> data to your structural (as your higher resolution more accurate scan
> is then the "gold standard" that others get matched to: though I
> don't
> know if there is any scientific validity to that claim). It also fits
> better with the general FreeSurfer approach (correct me if I'm wrong
> list). I would also recommend converting your dicoms to nii using
> mri_convert, because mri_convert has much broader support for the
> nifti format than the SPM tools for converting dicoms i.e. more
> coordinate frame information is included in a nifti generated by
> mri_convert than by the default SPM tools.
>
> D
>
> On Thu, Jan 19, 2012 at 11:59 AM, Léoné, F.T.M. (Frank)
> <f.le...@fcdonders.ru.nl> wrote:
> > Hi Dan,
> >
> > Sure. It was in my earlier e-mail of today: I use tksurfer, see
> below. For this last test, I used the SPM display function though,
> that now shows them to both have the same orientation, so appears to
> be okay. Or am I still missing something?
> >
> > best,
> >
> > Frank
> >
> > Hi Douglas,
> >
> > Ah, makes sense, sorry for that.
> >
> > I do most of the work in SPM, so:
> >
> > - I have a highres structural scan, nii file format
> > - I convert it to a surface using recon-all
> > - Coregister the highres structural to the functional scan, so it
> is
> > in the voxel size and orientation as the functional scans (SPM)
> > - I try to bbregister the coregistered and resliced T1 with the
> > surface using something like:
> > bbregister --s S7_FS --mov
> ~/Data/Exp1_Saccades_phase/S7_FS/mri/orig/flipped_rmasked_str_S2_seler20090508.nii
> --init-spm --reg
> ~/Data/Exp1_Saccades_phase/S7_FS/mri/orig/register.partial.auto.dat
> --t1
> > and view it with
> > vglrun tkregister2 --mov
> /home/action/fraleo/Data/Exp1_Saccades_phase/S7_FS/mri/orig/flipped_rmasked_str_S2_seler20090508.nii
> --reg
> /home/action/fraleo/Data/Exp1_Saccades_phase/S7_FS/mri/orig/register.partial.auto.dat
> --surf
> >
> > Here you see that I already use a flipped structural scan. If I do
> it like this, bbregister converges to a nice and correct solution
> (everything aligns). If I don't, tkregister2 showms unregistered struc
> and func, while it is obvious it would be roughly aligned if you would
> flip either of them.
> >
> > In addition/in general: What would be the recommended way to do the
> coregistration etc. if you do all you analyses in SPM? Would it for
> example be better to coregistrate and reslice all functionals with the
> structural, so they are automatically aligned with the surface? Now I
> have a structural which is coregistered with the funcional and I
> realign that one, but that makes for one extra step where it can go
> wrong. Don't think this is related to the flip, but I also have a few
> alignment problems for other subjects.
> >
> > Thanks a lot in advance,
> >
> > best,
> >
> > Frank
> > ----- "Dan Wakeman" <dgwake...@gmail.com> schreef:
> >
> >> Van: "Dan Wakeman" <dgwake...@gmail.com>
> >> Aan: "F.T.M. Léoné (Frank)" <f.le...@donders.ru.nl>
> >> Cc: freesurfer@nmr.mgh.harvard.edu
> >> Verzonden: Donderdag 19 januari 2012 17:09:28
> >> Onderwerp: Re: [Freesurfer] Freesurfer flips brains?
> >>
> >> Hi Frank,
> >>
> >> I think we still need to know. What software are you using to view
> the
> >> volumes?
> >>
> >> D
> >>
> >> On Thu, Jan 19, 2012 at 10:59 AM, Léoné, F.T.M. (Frank)
> >> <f.le...@fcdonders.ru.nl> wrote:
> >> > Hi Doug,
> >> >
> >> > Ah, I found the cause myself, which might be useful for others.
> It
> >> happens already in the first step, before the ones I listed: in
> >> mri_convert. I do:
> >> >
> >> > mri_convert struct.nii 001.mgz
> >> >
> >> > And it flips. This I can see because I converted the mgz back
> >> (mri_convert 001.mgz orig.nii) and then it's indeed reversed (and
> >> shifted, rotated, all rigid body transformations one can think
> of).
> >> Why does this happen? Is it normal for nii-files? I see that I can
> >> specify the orientation in mri_convert by doing mri_convert
> >> -in_orientation and then a three letter specification. I chose PSR
> and
> >> now the changes are far less severe (only a small shift still) and
> >> most importantly: no flip anymore. Do I now need to reconvert my
> all
> >> my surfaces? I don't hope, but I'm at least glad I have this one
> >> fixed.
> >> >
> >> > best,
> >> >
> >> > Frank
> >> >
> >> > ----- "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> schreef:
> >> >
> >> >> Van: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> >> >> Aan: "Frank Leoné" <f.le...@donders.ru.nl>
> >> >> Cc: freesurfer@nmr.mgh.harvard.edu
> >> >> Verzonden: Woensdag 18 januari 2012 18:34:31
> >> >> Onderwerp: Re: [Freesurfer] Freesurfer flips brains?
> >> >>
> >> >> Hi Frank, we'll need a lot more detail. Are you doing all of
> this
> >> in
> >> >> FreeSurfer? What are your command lines? How are you evaluating
> >> >> whether
> >> >> volumes are flipped?
> >> >> doug
> >> >>
> >> >> Léoné wrote:
> >> >> > Dear all,
> >> >> >
> >> >> > I must be missing something really obvious, but it seems my
> >> brains
> >> >> are flipped. What I do:
> >> >> >
> >> >> > - I have a highres structural scan, nii file format
> >> >> > - I convert it to a surface using recon-all
> >> >> > - Coregister the highres structural to the functional scan, so
> it
> >> is
> >> >> in the voxel size and orientation as the functional scans
> >> >> > - I try to bbregister the coregistered and resliced T1 with
> the
> >> >> surface
> >> >> >
> >> >> > But then: hey, it doesn't fit, my low-res T1 is flipped
> compared
> >> to
> >> >> my y surface, hence to my original T1. So is it indeed true that
> my
> >> T1
> >> >> might have been flipped? If so, does it make a wrong assumption
> on
> >> >> neurological vs radiological convention, or what is going on?
> >> >> >
> >> >> > Thanks in advance,
> >> >> >
> >> >> > best,
> >> >> >
> >> >> > Frank
> >> >> > _______________________________________________
> >> >> > Freesurfer mailing list
> >> >> > Freesurfer@nmr.mgh.harvard.edu
> >> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >> >> >
> >> >> >
> >> >> >
> >> >>
> >> >> --
> >> >> Douglas N. Greve, Ph.D.
> >> >> MGH-NMR Center
> >> >> gr...@nmr.mgh.harvard.edu
> >> >> Phone Number: 617-724-2358
> >> >> Fax: 617-726-7422
> >> >>
> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >> >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> >> >>
> >> >>
> >> >>
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> to
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